diff -Nru adapterremoval-2.2.2/AdapterRemoval.1 adapterremoval-2.2.3/AdapterRemoval.1 --- adapterremoval-2.2.2/AdapterRemoval.1 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/AdapterRemoval.1 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,357 @@ +.\" Man page generated from reStructuredText. +. +.TH "ADAPTERREMOVAL" "1" "Jan 22, 2019" "2.2.3" "AdapterRemoval" +.SH NAME +AdapterRemoval \- Fast short-read adapter trimming and processing +. +.nr rst2man-indent-level 0 +. +.de1 rstReportMargin +\\$1 \\n[an-margin] +level \\n[rst2man-indent-level] +level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] +- +\\n[rst2man-indent0] +\\n[rst2man-indent1] +\\n[rst2man-indent2] +.. +.de1 INDENT +.\" .rstReportMargin pre: +. RS \\$1 +. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] +. nr rst2man-indent-level +1 +.\" .rstReportMargin post: +.. +.de UNINDENT +. RE +.\" indent \\n[an-margin] +.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] +.nr rst2man-indent-level -1 +.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] +.in \\n[rst2man-indent\\n[rst2man-indent-level]]u +.. +.SH SYNOPSIS +.sp +\fBAdapterRemoval\fP [\fIoptions\fP…] –file1 <\fIfilenames\fP> [–file2 <\fIfilenames\fP>] +.SH DESCRIPTION +.sp +\fBAdapterRemoval\fP removes residual adapter sequences from single\-end (SE) or paired\-end (PE) FASTQ reads, optionally trimming Ns and low qualities bases and/or collapsing overlapping paired\-end mates into one read. Low quality reads are filtered based on the resulting length and the number of ambigious nucleotides (‘N’) present following trimming. These operations may be combined with simultaneous demultiplexing using 5’ barcode sequences. Alternatively, \fBAdapterRemoval\fP may attempt to reconstruct a consensus adapter sequences from paired\-end data, in order to allow the identification of the adapter sequences originally used. +.sp +If you use this program, please cite the paper: +.INDENT 0.0 +.INDENT 3.5 +Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 +.sp +\fI\%http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104\-016\-1900\-2\fP +.UNINDENT +.UNINDENT +.sp +For detailed documentation, please see +.INDENT 0.0 +.INDENT 3.5 +\fI\%http://adapterremoval.readthedocs.io/en/v2.2.3/\fP +.UNINDENT +.UNINDENT +.SH OPTIONS +.INDENT 0.0 +.TP +.B \-\-help +Display summary of command\-line options. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-version +Print the version string. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-file1 filename [filenames...] +Read FASTQ reads from one or more files, either uncompressed, bzip2 compressed, or gzip compressed. This contains either the single\-end (SE) reads or, if paired\-end, the mate 1 reads. If running in paired\-end mode, both \fB\-\-file1\fP and \fB\-\-file2\fP must be set. See the primary documentation for a list of supported formats. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-file2 filename [filenames...] +Read one or more FASTQ files containing mate 2 reads for a paired\-end run. If specified, \fB\-\-file1\fP must also be set. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-identify\-adapters +Attempt to build a consensus adapter sequence from fully overlapping pairs of paired\-end reads. The minimum overlap is controlled by \fB\-\-minalignmentlength\fP\&. The result will be compared with the values set using \fB\-\-adapter1\fP and \fB\-\-adapter2\fP\&. No trimming is performed in this mode. Default is off. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-threads n +Maximum number of threads. Defaults to 1. +.UNINDENT +.SS FASTQ options +.INDENT 0.0 +.TP +.B \-\-qualitybase base +The Phred quality scores encoding used in input reads \- either ‘64’ for Phred+64 (Illumina 1.3+ and 1.5+) or ‘33’ for Phred+33 (Illumina 1.8+). In addition, the value ‘solexa’ may be used to specify reads with Solexa encoded scores. Default is 33. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-qualitybase\-output base +The base of the quality score for reads written by AdapterRemoval \- either ‘64’ for Phred+64 (i.e., Illumina 1.3+ and 1.5+) or ‘33’ for Phred+33 (Illumina 1.8+). In addition, the value ‘solexa’ may be used to specify reads with Solexa encoded scores. However, note that quality scores are represented using Phred scores internally, and conversion to and from Solexa scores therefore result in a loss of information. The default corresponds to the value given for \fB\-\-qualitybase\fP\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-qualitymax base +Specifies the maximum Phred score expected in input files, and used when writing output files. Possible values are 0 to 93 for Phred+33 encoded files, and 0 to 62 for Phred+64 encoded files. Defaults to 41. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-mate\-separator separator +Character separating the mate number (1 or 2) from the read name in FASTQ records. Defaults to ‘/’. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-interleaved +Enables \fB\-\-interleaved\-input\fP and \fB\-\-interleaved\-output\fP\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-interleaved\-input +If set, input is expected to be a interleaved FASTQ files specified using \fB\-\-file1\fP, in which pairs of reads are written one after the other (e.g. read1/1, read1/2, read2/1, read2/2, etc.). +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-interleaved\-ouput +Write paired\-end reads to a single file, interleaving mate 1 and mate 2 reads. By default, this file is named \fBbasename.paired.truncated\fP, but this may be changed using the \fB\-\-output1\fP option. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-combined\-output +Write all reads into the files specified by \fB\-\-output1\fP and \fB\-\-output2\fP\&. The sequences of reads discarded due to quality filters or read merging are replaced with a single ‘N’ with Phred score 0. This option can be combined with \fB\-\-interleaved\-output\fP to write PE reads to a single output file specified with \fB\-\-output1\fP\&. +.UNINDENT +.SS Output file options +.INDENT 0.0 +.TP +.B \-\-basename filename +Prefix used for the naming output files, unless these names have been overridden using the corresponding command\-line option (see below). +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-settings file +Output file containing information on the parameters used in the run as well as overall statistics on the reads after trimming. Default filename is ‘basename.settings’. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-output1 file +Output file containing trimmed mate1 reads. Default filename is ‘basename.pair1.truncated’ for paired\-end reads, ‘basename.truncated’ for single\-end reads, and ‘basename.paired.truncated’ for interleaved paired\-end reads. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-output2 file +Output file containing trimmed mate 2 reads when \fB\-\-interleaved\-output\fP is not enabled. Default filename is ‘basename.pair2.truncated’ in paired\-end mode. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-singleton file +Output file to which containing paired reads for which the mate has been discarded. Default filename is ‘basename.singleton.truncated’. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-outputcollapsed file +If –collapsed is set, contains overlapping mate\-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low\-quality or ambiguous nucleotides. Default filename is ‘basename.collapsed’ +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-outputcollapsedtruncated file +Collapsed reads (see –outputcollapsed) which were trimmed due the presence of low\-quality or ambiguous nucleotides. Default filename is ‘basename.collapsed.truncated’. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-discarded file +Contains reads discarded due to the –minlength, –maxlength or –maxns options. Default filename is ‘basename.discarded’. +.UNINDENT +.SS Output compression options +.INDENT 0.0 +.TP +.B \-\-gzip +If set, all FASTQ files written by AdapterRemoval will be gzip compressed using the compression level specified using \fB\-\-gzip\-level\fP\&. The extension “.gz” is added to files for which no filename was given on the command\-line. Defaults to off. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-gzip\-level level +Determines the compression level used when gzip’ing FASTQ files. Must be a value in the range 0 to 9, with 0 disabling compression and 9 being the best compression. Defaults to 6. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-bzip2 +If set, all FASTQ files written by AdapterRemoval will be bzip2 compressed using the compression level specified using \fB\-\-bzip2\-level\fP\&. The extension “.bz2” is added to files for which no filename was given on the command\-line. Defaults to off. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-bzip2\-level level +Determines the compression level used when bzip2’ing FASTQ files. Must be a value in the range 1 to 9, with 9 being the best compression. Defaults to 9. +.UNINDENT +.SS FASTQ trimming options +.INDENT 0.0 +.TP +.B \-\-adapter1 adapter +Adapter sequence expected to be found in mate 1 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the “Adapters” section of the online documentation. Default is AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-adapter2 adapter +Adapter sequence expected to be found in mate 2 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the “Adapters” section of the online documentation. Default is AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-adapter\-list filename +Read one or more adapter sequences from a table. The first two columns (separated by whitespace) of each line in the file are expected to correspond to values passed to –adapter1 and –adapter2. In single\-end mode, only column one is required. Lines starting with ‘#’ are ignored. When multiple rows are found in the table, AdapterRemoval will try each adapter (pair), and select the best aligning adapters for each FASTQ read processed. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-minadapteroverlap length +In single\-end mode, reads are only trimmed if the overlap between read and the adapter is at least X bases long, not counting ambiguous nucleotides (N); this is independent of the \fB\-\-minalignmentlength\fP when using \fB\-\-collapse\fP, allowing a conservative selection of putative complete inserts in single\-end mode, while ensuring that all possible adapter contamination is trimmed. The default is 0. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-mm mismatchrate +The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If \fB\(ga\-\-mismatchrate\fP is greater than 1, the rate is set to 1 / \fB\-\-mismatchrate\fP\&. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using \fB\-\-identify\-adapters\fP\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-shift n +To allow for missing bases in the 5’ end of the read, the program can let the alignment slip \fB\-\-shift\fP bases in the 5’ end. This corresponds to starting the alignment maximum \fB\-\-shift\fP nucleotides into read2 (for paired\-end) or the adapter (for single\-end). The default is 2. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-trim5p n [n] +Trim the 5’ of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts. Off by default. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-trim3p n [n] +Trim the 3’ of reads by a fixed amount. See \fB\-\-trim5p\fP\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-trimns +Trim consecutive Ns from the 5’ and 3’ termini. If quality trimming is also enabled (\fB\-\-trimqualities\fP), then stretches of mixed low\-quality bases and/or Ns are trimmed. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-maxns n +Discard reads containing more than \fB\-\-max\fP ambiguous bases (‘N’) after trimming. Default is 1000. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-trimqualities +Trim consecutive stretches of low quality bases (threshold set by \fB\-\-minquality\fP) from the 5’ and 3’ termini. If trimming of Ns is also enabled (\fB\-\-trimns\fP), then stretches of mixed low\-quality bases and Ns are trimmed. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-trimwindows window_size +Trim low quality bases using a sliding window based approach inspired by \fBsickle\fP with the given window size. See the “Window based quality trimming” section of the manual page for a description of this algorithm. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-minquality minimum +Set the threshold for trimming low quality bases using \fB\-\-trimqualities\fP and \fB\-\-trimwindows\fP\&. Default is 2. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-minlength length +Reads shorter than this length are discarded following trimming. Defaults to 15. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-maxlength length +Reads longer than this length are discarded following trimming. Defaults to 4294967295. +.UNINDENT +.SS FASTQ merging options +.INDENT 0.0 +.TP +.B \-\-collapse +In paired\-end mode, merge overlapping mates into a single and recalculate the quality scores. In single\-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete “collapsed” reads are written with a ‘M_’ name prefix, and “collapsed” reads which are trimmed due to quality settings are written with a ‘MT_’ name prefix. The overlap needs to be at least \fB\-\-minalignmentlength\fP nucleotides, with a maximum number of mismatches determined by \fB\-\-mm\fP\&. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-minalignmentlength length +The minimum overlap between mate 1 and mate 2 before the reads are collapsed into one, when collapsing paired\-end reads, or when attempting to identify complete template sequences in single\-end mode. Default is 11. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-seed seed +When collaping reads at positions where the two reads differ, and the quality of the bases are identical, AdapterRemoval will select a random base. This option specifies the seed used for the random number generator used by AdapterRemoval. This value is also written to the settings file. Note that setting the seed is not reliable in multithreaded mode, since the order of operations is non\-deterministic. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-deterministic +Enable deterministic mode; currently only affects –collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. +.UNINDENT +.SS FASTQ demultiplexing options +.INDENT 0.0 +.TP +.B \-\-barcode\-list filename +Perform demultiplxing using table of one or two fixed\-length barcodes for SE or PE reads. The table is expected to contain 2 or 3 columns, the first of which represent the name of a given sample, and the second and third of which represent the mate 1 and (optionally) the mate 2 barcode sequence. For a detailed description, see the “Demultiplexing” section of the online documentation. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-barcode\-mm n +.TP +.B Maximum number of mismatches allowed when counting mismatches in both the mate 1 and the mate 2 barcode for paired reads. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-barcode\-mm\-r1 n +Maximum number of mismatches allowed for the mate 1 barcode; if not set, this value is equal to the \fB\-\-barcode\-mm\fP value; cannot be higher than the \fB\-\-barcode\-mm\fP value. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-barcode\-mm\-r2 n +Maximum number of mismatches allowed for the mate 2 barcode; if not set, this value is equal to the \fB\-\-barcode\-mm\fP value; cannot be higher than the \fB\-\-barcode\-mm\fP value. +.UNINDENT +.INDENT 0.0 +.TP +.B \-\-demultiplex\-only +Only carry out demultiplexing using the list of barcodes supplied with –barcode\-list. No other processing is done. +.UNINDENT +.SH WINDOW BASED QUALITY TRIMMING +.sp +As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base\-trimming inspired by \fBsickle\fP\&. If \fBwindow_size\fP is greater than or equal to 1, that number is used as the window size for all reads. If \fBwindow_size\fP is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. +.sp +Reads are trimmed as follows for a given window size: +.INDENT 0.0 +.INDENT 3.5 +.INDENT 0.0 +.IP 1. 3 +The new 5’ is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than \fB\-\-minquality\fP\&. +.IP 2. 3 +The new 3’ is located by sliding the first window right, until the average quality becomes less than or equal to \fB\-\-minquality\fP\&. The new 3’ is placed at the last base in that window where the quality is greater than or equal to \fB\-\-minquality\fP\&. +.IP 3. 3 +If no 5’ position could be determined, the read is discarded. +.UNINDENT +.UNINDENT +.UNINDENT +.SH EXIT STATUS +.sp +AdapterRemoval exists with status 0 if the program ran succesfully, and with a non\-zero exit code if any errors were encountered. Do not use the output from AdapterRemoval if the program returned a non\-zero exit code! +.SH REPORTING BUGS +.sp +Please report any bugs using the AdapterRemoval issue\-tracker: +.sp +\fI\%https://github.com/MikkelSchubert/adapterremoval/issues\fP +.SH LICENSE +.sp +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 3 of the License, or +at your option any later version. +.sp +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +.sp +You should have received a copy of the GNU General Public License +along with this program. If not, see <\fI\%http://www.gnu.org/licenses/\fP>. +.SH AUTHOR +Mikkel Schubert; Stinus Lindgreen +.SH COPYRIGHT +2017, Mikkel Schubert; Stinus Lindgreen +.\" Generated by docutils manpage writer. +. diff -Nru adapterremoval-2.2.2/AdapterRemoval.pod adapterremoval-2.2.3/AdapterRemoval.pod --- adapterremoval-2.2.2/AdapterRemoval.pod 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/AdapterRemoval.pod 1970-01-01 00:00:00.000000000 +0000 @@ -1,467 +0,0 @@ -#!/usr/bin/perl -w - -=head1 NAME - -AdapterRemoval - Remove adapters from sequences in either single end or paired end experiments - -=head1 SYNOPSIS - -B --file1 filenames [--file2 filenames] [--interleaved] [--interleaved-input] [--interleaved-output] [--combined-output] [--basename filename] [--identify-adapters] [--trimns] [--maxns max] [--trimqualities] [--trimwindows length] [--minquality minimum] [--collapse] [--version] [--mm mismatchrate] [--minlength len] [--minalignmentlength len] [--qualitybase base] [--qualitybase-output base] [--shift num] [--adapter1 sequence] [--adapter2 sequence] [--adapter-list filename] [--barcode-list filename] [--barcode-mm num] [--barcode-mm-r1 num] [--barcode-mm-r2 num] [--demultiplex-only] [--output1 filename] [--output2 filename] [--singleton filename] [--outputcollapsed filename] [--outputcollapsedtruncated filename] [--discarded filename] [--settings filename] [--seed seed] [--gzip] [--gzip-level level] [--threads num] [--version] [--help] - - -=head1 DESCRIPTION - -B reads either one FASTQ file (single ended mode) or two FASTQ files (paired ended mode). It removes the residual adapter sequence from the reads and optionally trims Ns from the reads, and low qualities bases using the quality string, and collapses overlapping paired ended mates into one read. Reads are discarded if the remaining genomic part is too short, or if the read contains more than an (user specified) amount of amigious nucleotides ('N'). These operations may be combined with simultaneous demultiplexing. Alternatively, B may attempt to reconstruct a consensus adapter sequences from paired-ended data, in order to allow the identification of the adapter sequences originally used, and thereby ensure proper trimming of these reads. - -The reads and adapters are transformed to upper case for comparison. It is assumed that the letter 'N' is used for an unknown nucleotide, but in case the program encounters a '.' in the sequence, they will be treated as (and translated into) Ns. The program tries to check for invalid input and / or nonsensical combinations of parameters but please report strange behaviour, bugs and such to MikkelSch@gmail.com - -If you use this program, please cite the paper: - -Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 -http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 - -=head1 OPTIONS - -=over 9 - -=item B<--file1> I [...] - -Read FASTQ reads from one or more files. This contains either the single ended (SE) reads or, if paired ended, the mate 1 reads. If running in paired end mode, both I<--file1> and I<--file2> must be set. The files may optionally be gzip or bzip2 compressed. - -=item B<--file2> I [...] - -Read one or more FASTQ files containing mate 2 reads for a paired end run. If specified, --file1 must also be set. The files may optionally be gzip or bzip2 compressed. - -=item B<--interleaved> - -Enables I<--interleaved-input> and I<--interleaved-output>. - -=item B<--interleaved-input> - -If set, input is expected to be a single FASTQ file specified using I<--file1>, in which pairs of paired-end reads are listed one after each other (read1/1, read1/2, read2/1, read2/2, etc.). - -=item B<--interleaved-ouput> - -If set, and AdapterRemoval is processing paired-end reads, retained pairs of reads are written to a single FASTQ file, one pair after each other (read1/1, read1/2, read2/1, read2/2, etc.). By default, this file is named I, but this may be changed using the I<--output1> option. - -=item B<--combined-output> - -If set, all reads are written to the same file(s), specified by --output1 and --output2. Each read is further marked by either a "PASSED" or a "FAILED" flag, and any read that has been FAILED (including the mate for collapsed reads) are replaced with a single 'N' with Phred score 0. This option can be combined with --interleaved / --interleaved-output to write all reads to a single output file specified with --output1. - -=item B<--basename> I - -Determines the default filename for output files, unless overridden using the specific output file settings. For single-ended mode, the following filenames are used: I, I, and I. In paired end mode, the following filenames are used: I, I, I, I, and I. If collapsing of reads is enabled for paired ended mode, the following filenames are also used: I, and I. The default basename is I. If gzip compression is enabled, the extension ".gz" is added to all files but the I file, while the extension ".bz2" is used if bzip2 compression is enabled. - -=item B<--identify-adapters> - -For paired ended reads only. In this mode, AdapterRemoval will attempt to reconstruct the adapter sequences used for a set of paired ended reads, by locating fully overlapping read-pairs, and generating a consensus sequence from the bases identified as adapter sequence. The minimum overlap is controlled by I. The values passed to the --adapter1 and --adapter2 command-line options are used for visual comparison with the consensus sequence, but otherwise not used in the consensus building. - -=item B<--trimns> - -Remove stretches of Ns from the output reads in both the 5' and 3' end. If quality trimming is also enabled, stretches of mixed low-quality bases and/or Ns are trimmed. - -=item B<--maxns> I - -If a read has more than I Ns after trimming, it is discarded (default is not to use). - -=item B<--trimqualities> - -Remove consecutive stretches of low quality bases (threshold set by I) from both the 5' and 3' end of the reads. All bases with I or lower are trimmed. If trimming of Ns is also enabled, stretches of mixed low-quality bases and/or Ns are trimmed. - -=item B<--trimwindows> I - -Remove low quality bases using a sliding window bases approach inspired by B: - -B<1.> The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than I. - -B<2.> The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to I. The new 3' is placed at the last base in that window where the quality is greater than or equal to I. - -B<3.> If no 5' position could be determined, the read is discarded. - -The value of I may be a number greater than or equal to 1, in which case that number (rounded down to the nearest whole number) is used as the window length, or it may be a value greater than or equal to zero. In the latter case, that number is multipled by the lenght of each read, to determine the window length. For example, a I value of 0.1 and a read length of 100 would result in 10 bp windows. If the resulting window length is zero or is greater than the current read length, then the read length is used instead. - -=item B<--minquality> I - -Set the threshold for trimming low quality bases. Default is 2. The minimum can be set with or without the Phred quality base. - -=item B<--collapse> - -In paired-end mode, if the two mates overlap, collapse the two reads into one read by merging the two and recalculating the quality scores. In single-end mode, this instead attempts to identify templates for which the entire sequence is available. In both cases, complete "collapsed" reads are written with a 'M_' name prefix, and "collapsed" reads which are trimmed due to quality settings are written with a 'MT_' name prefix. The overlap needs to be at least I nucleotides, with a maximum number of mismatches determined by I. - -=item B<--mm> I - -The allowed fraction of mismatches allowed in the aligned region. If 0 < I < 1, the rate is used directly. If I > 1, the rate is set to 1/I. The default setting is 3, corresponding to a maximum mismatch rate of 1/3. - -=item B<--minlength> I - -The minimum length required after trimming and adapter removal. Reads shorter than I are discarded. Default is 15 nucleotides. - -=item B<--minalignmentlength> I - -The minimum overlap between mate 1 and mate 2 before the reads are collapsed into one, when collapsing paired end reads, or when attempting to identify complete template sequences in single-end mode. Default is 11 nucleotides. - -=item B<--qualitybase> I - -The base of the quality score - either '64' for Phred+Phred (i.e., Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. Default is 33. - -=item B<--qualitybase-output> I - -The base of the quality score for reads written by AdapterRemoval - either '64' for Phred+Phred (i.e., Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. However, note that quality scores are represented using PHRED scores internally, and conversion to and from Solexa scores therefore result in a loss of information. The default corresponds to the value given for --qualitybase. - -=item B<--shift> I - -To allow for missing bases in the 5' end of the read, the program can let the alignment slip I bases in the 5' end. This corresponds to starting the alignment maximum I nucleotides in read2 (for paired end) or the adapter (for single end). The default shift valule is 2. - -=item B<--adapter1> I - -=item B<--adapter2> I - -Specify the adapter sequences that you wish to trim. The Adapter #2 sequence is only used when trimming paired-ended data. - -The Adapter #1 and Adapter #2 sequences are expected to be found in the mate 1 and the mate 2 reads respectively, while ignoring any difference in case and treating Ns as wildcards. The default sequences are - -Adapter #1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG - -Adapter #2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - -Assuming these were the adapters used to generate our data, we should therefore see these in the FASTQ files: - - $ grep -i "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC......ATCTCGTATGCCGTCTTCTGCTTG" file1.fq - BAAAAAAAAACAAGAAT - CTGGAGTTCBAAAAAAA - GGBCAAATTGAAAACAC - ... - - $ grep -i "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" file2.fq - CBCAAAAAAAGAAAAACATCTTG - GAACTCCAGBCAAAAAAAATAGA - GAACTBCAAAAACATAAGACCTA - ... - -Note that --adapter1 and --adapter2 replaces the --pcr[12] options of B v1.x, for which the --pcr2 sequence was expected to be reverse complemented compared --adaper2. Using the --pcr[12] options is not recommended! - - -=item B<--adapter-list> I - -Read one or more PCR sequences from a table. The first two columns (separated by whitespace) of each line in the file are expected to correspond to values passed to --adapter1 and --adapter2. In single ended mode, only column one is required. Lines starting with '#' are ignored. When multiple PCR sequences or sequence pairs are specified, AdapterRemoval will try each adapter (pair) listed in the table, and select the best aligning adapters for each read processed. - -=item B<--barcode-list> I - -Read a table of one or two fixed-length barcodes and perform demultiplexing of single or double indexed reads. The table is expected to contain 2 or 3 columns, the first of which represent the name of a given sample, and the second and third of which represent the mate 1 and (optionally) the mate 2 barcode sequence: - - $ cat barcodes.txt - sample_1 ATGCGGA TGAATCT - sample_2 ATGGATT ATAGTGA - sample_7 CAAAACT TCGCTGC - -Results are written to ${basename}.${sample_name}.*, using the default names for other output files. A setting file with statistics is written for each sample at ${basename}.${sample_name}.settings, as is a setting file containing the demultiplexing statistics, at ${basename}.settings. - -When demultiplexing is used, the barcode identified for a given read is automatically added to the adapter sequence, in order to ensure that overlapping reads are correctly trimmed. The .settings file represents this by showing the reverse complemented) barcode sequence added to the --adapter1 and --adapter2 sequences, followed by an underscore (shown here for barcodes pair ATGCGGA / TGAATCT): - - [Adapter sequences] - Adapter1[0]: AGATTCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG - Adapter2[0]: TCCGCAT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - -Note that the sequence added to each adapter is the reverse complement of the barcode sequence of the other mate, as this sequence is expected to be found immediately before the adapter sequence. - - -=item B<--barcode-mm> I - -The maximum number of mismatches allowed for barcodes, when counting mismatches in I the mate 1 and mate 2 barcodes. In conjunction with the --barcode-mm-r1 and --barcode-mm-r2, this allows fine-grained control over the barcode comparisons. If not set, this value is set to the sum of --barcode-mm-r1 and --barcode-mm-r2. - -For example, to allow one mismatch in either the mate 1 or the mate 2 barcode, one might specify --barcode-mm 1; to allow a mismatch in the mate 1 and / or the mate 2 barcode, one might specify --barcode-mm 2 --barcode-mm-r1 1 --barcode-mm-r2 1, and so on. - -=item B<--barcode-mm-r1> I - -The maximum number of mismatches allowed in the mate 1 barcode; if not set, this number is equal to the value of --barcode-mm. This number cannot exceed the value specified for --barcode-mm. - -=item B<--barcode-mm-r2> I - -The maximum number of mismatches allowed in the mate 1 barcode; if not set, this number is equal to the value of --barcode-mm. This number cannot exceed the value specified for --barcode-mm. - -=item B<--demultiplex-only> I - -Only carry out demultiplexing, using the list of barcodes supplied using --barcode-list. Note that trimming and filtering options do not apply to this mode of operation. - -=item B<--output1> I - -=item B<--output2> I - -=item B<--singleton> I - -=item B<--outputcollapsed> I - -=item B<--outputcollapsedtruncated> I - -=item B<--discarded> I - -=item B<--settings> I - -Instead of using the default behaviour where the program automatically generates the files needed, you can specify where each type of output is directed. This can be files, pipes etc. thus making it possible to easily zip the output on the fly. Default files are still generated if nothing else is specified. - -The types of output in single end mode are: - -I contains the trimmed reads. - -The types of output in paired end mode are: - -I contains trimmed mate1 reads. - -I contains trimmed mate2 reads. - -I contains all reads where the other mate in a pair is discarded. - -I Contains pairs that overlap and are collapsed into a single read (if I<--collapse> is used). The reads are renamed with an @M_ prefix. - -I Contains pairs that overlap and are collapsed into a single read (if I<--collapse> is used) and have further been trimmed due to Ns and/or low quality nucleotides in the 5' or 3' end. The reads are renamed with an @MT_ prefix. - -The types of output in both single end and paired end mode are: - -I contains all reads that are discarded by the program. - -I contains information on the parameters used in the run as well as overall statistics on the reads after trimming such as average length. - -=item B<--seed> I - -When collaping reads at positions where the two reads differ, and the quality of the bases are identical, AdapterRemoval will select a random base. This option specifies the seed used for the random number generator used by AdapterRemoval. This value is also written to the settings file. Note that setting the seed is not reliable in multithreaded mode, since the order of operations is non-deterministic. - -=item B<--gzip> - -If set, all FASTQ files written by AdapterRemoval will be gzip compressed using the compression level specified using I<--gzip-level>. The extension ".gz" is added to files for which no filename was given on the commandline. - -=item B<--gzip-level> - -Determines the compression level used when gzip'ing FASTQ files. Must be a value in the range 0 to 9, with 0 disabling compression and 9 being the best compression. Defaults to 6. - -=item B<--bzip2> - -If set, all FASTQ files written by AdapterRemoval will be bzip2 compressed using the compression level specified using I<--bzip2-level>. The extension ".bz2" is added to files for which no filename was given on the commandline. - -=item B<--bzip2-level> - -Determines the compression level used when bzip2'ing FASTQ files. Must be a value in the range 1 to 9, with 9 being the best compression. Defaults to 9. - - -=item B<--threads> - -Maximum number of threads to use for current run; note that file IO is single-threaded, regardless of the number of threads specified. - -=item B<--version> - -Output the version of the program. - -=item B<--help> - -Output the summary of available command-line options, including default values and/or values specified on the command-line. - - -=back - - -=head1 EXAMPLE: Single end experiment - -The following command removes adapters from the file I trims both Ns and low quality bases from the reads, and gzip compresses the resulting files. The --basename option is used to specify the prefix for output files. - - $ AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip - -Since --gzip and --basename is specified, the trimmed FASTQ reads are written to I, the dicarded FASTQ reads are written to I, and settings and summary statistics are written to I. - -Note that by default, AdapterRemoval does not require a minimum number of bases overlapping with the adapter sequence, before reads are trimmed. This may result in an excess of very short (1 - 3 bp) 3' fragments being falsely identified as adapter sequences, and trimmed. This behavior may be changed using the --minadapteroverlap option, which allows the specification of a minimum number of bases (excluding Ns) that must be aligned to carry trimming. For example, use --minadapteroverlap 3 to require an overlap of at least 3 bp. - - -=head1 EXAMPLE: Paired end experiment. - -The following command removes adapters from a paired-end reads, where the mate 1 and mate 2 reads are kept in files I and I, respectively. The reads are trimmed for both Ns and low quality bases, and overlapping reads (at least 11 nucleotides, per default) are merged (collapsed): - - $ AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse - -This command generates the files I and I, which contain trimmed pairs of reads which were not collapsed, I containing reads where one mate was discarded, I containing merged reads, and I containing merged reads that have been trimmed due to the --trimns or --trimqualities options. Finally, the I and I files correspond to those of the single-end run. - - -=head1 EXAMPLE: Interleaved FASTQ reads. - -AdapterRemoval is able to read and write paired-end reads stored in a single, so-called interleaved FASTQ file (one pair at a time, first mate 1, then mate 2). This is accomplished by specifying the location of the file using I<--file1> and *also* setting the I<--interleaved> command-line option: - - $ AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved - -Other than taking just a single input file, this mode operates almost exactly like paired end trimming (as described above); the mode differs only in that paired reads are not written to a 'pair1' and a 'pair2' file, but instead these are instead written to a single, interleaved file, named 'paired'. The location of this file is controlled using the I<--output1> option. Enabling either reading or writing of interleaved FASTQ files, both not both, can be accomplished by specifying the either of the I<--interleaved-input> and I<--interleaved-output> options, both of which are enabled by the I<--interleaved> option. - - -=head1 EXAMPLE: Different quality score encodings. - -By default, AdapterRemoval expects the quality scores in FASTQ reads to be Phred+33 encoded, meaning that the error probabilities are encoded as (char)('!' - 10 * log10(p)). Most data will be encoded using Phred+33, but Phred+64 and 'Solexa' encoded quality scores are also supported. These are selected by specifying the I<--qualitybase> command-line option (specifying either '33', '64', or 'solexa'):: - - $ AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename phred_64_encoded - -By default, reads are written using the *same* encoding as the input. If a different encoding is desired, this may be accomplished using the I<--qualitybase-output> option: - - $ AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename phred_33_encoded - -Note furthermore that AdapterRemoval by default only expects quality scores in the range 0 - 41 (or -5 to 41 in the case of Solexa encoded scores). If input data using a different maximum quality score is to be processed, or if the desired maximum quality score of collapsed reads is greater than 41, then this limit may be increased using the I<--qualitymax> option: - - $ AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapsed --basename collapsed_q50 - -For a detailed overview of Phred encoding schemes currently and previously in use, see e.g. the Wikipedia article on the subject: -https://en.wikipedia.org/wiki/FASTQ_format#Encoding - - -=head1 EXAMPLE: Paired end reads containing multiple, distinct adapter pairs. - -It is possible to trim data that contains multiple adapter pairs, by providing a one or two-column table containing possible adapter combinations (for single-end and paired-end trimming, respectively; see e.g. I): - - $ cat adapters.txt - AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG - CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG - GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG - CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA - -This table is then specified using the I<--adapter-list> option: - - $ AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt - -The resulting .summary file contains an overview of how frequently each adapter (pair) was used. - -Note that in the case of paired-end adapters, AdapterRemoval considers only the combinations of adapters specified in the table, one combination per row. For single-end trimming, only the first column of the table file is required, and the list may therefore take the form of a file containing one sequence per line. - - - -=head1 EXAMPLE: Identifying adapter sequences from paired-ended reads - -If we did not know the adapter sequences for paired-end reads, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adpater sequence (not counting differences in index sequences). - -In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the I<--adapter1> or I<--adapter2> command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA: - - $ AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq - - Attemping to identify adapter sequences ... - Processed a total of 1,000 reads in 0.0s; 129,000 reads per second on average ... - Found 394 overlapping pairs ... - Of which 119 contained adapter sequence(s) ... - - Printing adapter sequences, including poly-A tails: - --adapter1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG - ||||||||||||||||||||||||||||||||||******|||||||||||||||||||||||| - Consensus: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA - Quality: 55200522544444/4411330333330222222/1.1.1.1111100-00000///..+....--*-)),,+++++++**(('%%%$ - - Top 5 most common 9-bp 5'-kmers: - 1: AGATCGGAA = 96.00% (96) - 2: AGATGGGAA = 1.00% (1) - 3: AGCTCGGAA = 1.00% (1) - 4: AGAGCGAAA = 1.00% (1) - 5: AGATCGGGA = 1.00% (1) - - - --adapter2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| - Consensus: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA - Quality: 525555555144141441430333303.2/22-2/-1..11111110--00000///..+....--*-),,,+++++++**(%'%%%$ - - Top 5 most common 9-bp 5'-kmers: - 1: AGATCGGAA = 100.00% (100) - -No files are generated from running the adapter identification step. - -The consensus sequences inferred are compared to those specified using the I<--adapter1> and I<--adapter2> command-line options, or with the default values for these if no values have been given (as in this case). Pipes (|) indicate matches between the provided sequences and the consensus sequence, and "*" indicate the presence of unspecified bases (Ns). - - - -=head1 EXAMPLE: Demultiplexing of paired end reads - -As of version 2.1, AdapterRemoval supports simultanious demultiplexing and adapter trimming; demultiplexing is carried out using a simple comparison between the specified barcode sequences and the first N bases of the reads, corresponding to the length of the barcodes. Reads identified as containing a specific barcode or pair of barcodes are then trimmed using adapter sequences including these barcodes. - -Demultiplexing is enabled by creating a table of barcodes, the first column of which species the sample name (using characters [a-zA-Z0-9_]) and the second and (optional) third columns specifies the mate 1 and mate 2 barcode sequences. - -For example, a table of barcodes from a double-indexed run might be as follows (see I): - - $ cat barcodes.txt - sample_1 ATGCGGA TGAATCT - sample_2 ATGGATT ATAGTGA - sample_7 CAAAACT TCGCTGC - -In the case of single-read reads, only the first two columns are required. AdapterRemoval is invoked with the I<--barcode-list> option, specifying the path to this table: - - $ AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_dumux --barcode-list barcodes.txt - -This generates a set of output files for each sample specified in the barcode table, using the basename (I<--basename>) as the prefix, followed by a dot and the sample name, followed by a dot and the default name for a given file type. For example, the output files for sample_2 would be - - output_demux.sample_2.discarded - output_demux.sample_2.pair1.truncated - output_demux.sample_2.pair2.truncated - output_demux.sample_2.settings - output_demux.sample_2.singleton.truncated - -The settings files generated for each sample summarizes the reads for that sample only; in addition, a basename.settings file is generated which summarizes the number and proportion of reads identified as belonging to each sample. - -The maximum number of mismatches allowed when comparing barocdes is controlled using the options I<--barcode-mmI>, I<--barcode-mm-r1>, and I<--barcode-mm-r2>, which specify the maximum number of mismatches total, and the maximum number of mismatches for the mate 1 and mate 2 barcodes respectively. Thus, if mm_1(i) and mm_2(i) represents the number of mismatches observed for barcode-pair i for a given pair of reads, these options require that - - 1. mm_1(i) <= --barcode-mm-r1 - 2. mm_2(i) <= --barcode-mm-r2 - 3. mm_1(i) + mm_2(i) <= --barcode-mm - -As of version 2.2, AdapterRemoval can furthermore be used to demultiplex reads without carrying out other forms of read trimming. This is accomplished by specifying the I<--demultiplex-only> option: - - $ AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only - -Trimming and filtering related options to not apply to this mode ("TRIMMING SETTINGS" when viewing 'AdapterRemoval --help'), but compression (I<--gzip>, I<--bzip2>), multi-threading (I<--threads>), interleaving (I<--interleaved>, etc.) and other such options may be used in conjunction with --demultiplex-only. - - -=head1 EXIT STATUS - -0 if everything worked as planned, a non-zero value otherwise. - -=head1 REPORTING BUGS - -Report bugs to Mikkel Schubert . - -Your bugreport should always include: - -=over 2 - -=item * - -The output of B. If you are not running the -latest released version you should specify why you believe the problem -is not fixed in that version. - -=item * - -A complete example that others can run that shows the problem. - -=back - - -=head1 AUTHOR - -Copyright (C) 2011 Stinus Lindgreen . - -Parts of the manual was written by Ole Tange . - -Parts of the manual was written by Mikkel Schubert . - - -=head1 LICENSE - -Copyright (C) 2011 Stinus Lindgreen . - -Copyright (C) 2014 Mikkel Schubert . - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; either version 3 of the License, or -at your option any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=head1 SEE ALSO - - - -=cut diff -Nru adapterremoval-2.2.2/CHANGES.md adapterremoval-2.2.3/CHANGES.md --- adapterremoval-2.2.2/CHANGES.md 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/CHANGES.md 2019-01-22 21:39:48.000000000 +0000 @@ -1,3 +1,20 @@ +### Version 2.2.3 - 2019-01-22 + + * Added support for trimming reads by a fixed amount: --trim5p N --trim3p N. + Different values may be given for each mate: --trim5p N1 N2. Trimming is + carried out after adapters have been removed and reads have been collapsed, + if enabled, but before quality trimming (Ns and low qualities). + * Added option for determistic read merging (--collapse-deterministic). In + this mode AdapterRemoval will set a merged base to 'N' with quality 0 if + the corresponding bases on the two mates differ, and if both have the same + quality score. The default behavior is to select one of the two bases at + random. + * Fixed reporting of line numbers in error messages. + * Added conda installation instructions, courtesy of Maxime Borry (maxibor). + * Fixed reading mate 2 adapters specified via --adapter-list. Adapters would + be used in the reverse orientation compared to --adapter2. Courtesy of + Karolis (KarolisM). + * Fixed various typos and improved help/error messages. ### Version 2.2.2 - 2017-07-17 diff -Nru adapterremoval-2.2.2/debian/adapterremoval.manpages adapterremoval-2.2.3/debian/adapterremoval.manpages --- adapterremoval-2.2.2/debian/adapterremoval.manpages 2018-09-21 06:19:48.000000000 +0000 +++ adapterremoval-2.2.3/debian/adapterremoval.manpages 2019-01-27 11:29:03.000000000 +0000 @@ -1 +1 @@ -build/AdapterRemoval.1 +AdapterRemoval.1 diff -Nru adapterremoval-2.2.2/debian/changelog adapterremoval-2.2.3/debian/changelog --- adapterremoval-2.2.2/debian/changelog 2018-09-21 06:19:48.000000000 +0000 +++ adapterremoval-2.2.3/debian/changelog 2019-01-27 11:29:03.000000000 +0000 @@ -1,3 +1,12 @@ +adapterremoval (2.2.3-1) unstable; urgency=medium + + * New upstream version + * debhelper 12 + * Standards-Version: 4.3.0 + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target + + -- Andreas Tille Sun, 27 Jan 2019 12:29:03 +0100 + adapterremoval (2.2.2-2) unstable; urgency=medium [ Steffen Moeller ] diff -Nru adapterremoval-2.2.2/debian/compat adapterremoval-2.2.3/debian/compat --- adapterremoval-2.2.2/debian/compat 2018-09-21 06:19:48.000000000 +0000 +++ adapterremoval-2.2.3/debian/compat 2019-01-27 11:29:03.000000000 +0000 @@ -1 +1 @@ -11 +12 diff -Nru adapterremoval-2.2.2/debian/control adapterremoval-2.2.3/debian/control --- adapterremoval-2.2.2/debian/control 2018-09-21 06:19:48.000000000 +0000 +++ adapterremoval-2.2.3/debian/control 2019-01-27 11:29:03.000000000 +0000 @@ -4,12 +4,12 @@ Kevin Murray Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper (>= 12~), zlib1g-dev, libbz2-dev, libgtest-dev, python-markdown -Standards-Version: 4.2.1 +Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/adapterremoval Vcs-Git: https://salsa.debian.org/med-team/adapterremoval.git Homepage: https://github.com/MikkelSchubert/adapterremoval diff -Nru adapterremoval-2.2.2/debian/rules adapterremoval-2.2.3/debian/rules --- adapterremoval-2.2.2/debian/rules 2018-09-21 06:19:48.000000000 +0000 +++ adapterremoval-2.2.3/debian/rules 2019-01-27 11:29:03.000000000 +0000 @@ -14,8 +14,10 @@ markdown_py -f README.html README.md override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) # dh_auto_test echo "*********** Needs adapting to libgtest-dev. ***************" +endif override_dh_auto_install: make PREFIX=$(CURDIR)/debian/$(DEB_SOURCE)/usr diff -Nru adapterremoval-2.2.2/docs/conf.py adapterremoval-2.2.3/docs/conf.py --- adapterremoval-2.2.2/docs/conf.py 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/conf.py 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,171 @@ +# -*- coding: utf-8 -*- +# +# AdapterRemoval documentation build configuration file, created by +# sphinx-quickstart on Sun Sep 17 15:00:32 2017. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +# import os +# import sys +# sys.path.insert(0, os.path.abspath('.')) + + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'AdapterRemoval' +copyright = u'2017, Mikkel Schubert; Stinus Lindgreen' +author = u'Mikkel Schubert; Stinus Lindgreen' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = u'2.2.3' +# The full version, including alpha/beta/rc tags. +release = u'2.2.3' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = [] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'alabaster' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +# html_theme_options = {} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# This is required for the alabaster theme +# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars +html_sidebars = { + '**': [ + 'about.html', + 'navigation.html', + 'relations.html', # needs 'show_related': True theme option to display + 'searchbox.html', + 'donate.html', + ] +} + + +# -- Options for HTMLHelp output ------------------------------------------ + +# Output file base name for HTML help builder. +htmlhelp_basename = 'AdapterRemovaldoc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'AdapterRemoval.tex', u'AdapterRemoval Documentation', + author, 'manual'), +] + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('manpage', 'AdapterRemoval', u'Fast short-read adapter trimming and processing', + [author], 1) +] + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'AdapterRemoval', u'AdapterRemoval Documentation', + author, 'AdapterRemoval', 'One line description of project.', + 'Miscellaneous'), +] + + + diff -Nru adapterremoval-2.2.2/docs/examples.rst adapterremoval-2.2.3/docs/examples.rst --- adapterremoval-2.2.2/docs/examples.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/examples.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,191 @@ +.. highlight:: Bash + + +Example usage +============= + +The following examples all make use of the data included in the 'examples' folder. + + +Trimming single-end reads +------------------------- + +The following command removes adapters from the file *reads_1.fq* trims both Ns and low quality bases from the reads, and gzip compresses the resulting files. The ``--basename`` option is used to specify the prefix for output files:: + + AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip + +Since ``--gzip`` and ``--basename`` is specified, the trimmed FASTQ reads are written to *output_single.truncated.gz*, the discarded FASTQ reads are written to *output_single.discarded.gz*, and settings and summary statistics are written to *output_single.settings*. + +Note that by default, AdapterRemoval does not require a minimum number of bases overlapping with the adapter sequence, before reads are trimmed. This may result in an excess of very short (1 - 3 bp) 3' fragments being falsely identified as adapter sequences, and trimmed. This behavior may be changed using the ``--minadapteroverlap`` option, which allows the specification of a minimum number of bases (excluding Ns) that must be aligned to carry trimming. For example, use *--minadapteroverlap 3* to require an overlap of at least 3 bp. + + +Trimming paired-end reads +------------------------- + +The following command removes adapters from a paired-end reads, where the mate 1 and mate 2 reads are kept in files *reads_1.fq* and *reads_2.fq*, respectively. The reads are trimmed for both Ns and low quality bases, and overlapping reads (at least 11 nucleotides, per default) are merged (collapsed):: + + AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse + +This command generates the files *output_paired.pair1.truncated* and *output_paired.pair2.truncated*, which contain trimmed pairs of reads which were not collapsed, *output_paired.singleton.truncated* containing reads where one mate was discarded, *output_paired.collapsed* containing merged reads, and *output_paired.collapsed.truncated* containing merged reads that have been trimmed due to the ``--trimns`` or ``--trimqualities`` options. Finally, the *output_paired.discarded* and *output_paired.settings* files correspond to those of the single-end run. + + +Multiple input FASTQ files +-------------------------- + +More than one input file may be specified for mate 1 and mate 2 reads. This is accomplished simply by listing more than one file after the ``--file1`` and the ``--file2`` options. + +For single-end reads:: + + AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq + +And for paired-end reads:: + + AdapterRemoval --file1 reads_1a.fq reads_1b.fq reads_1c.fq --file2 reads_2a.fq reads_2b.fq reads_2c.fq + +AdapterRemoval will process these files as if they had been concatenated into a single file or pair of files prior to invoking AdapterRemoval. For paired reads, the files must be specified in the same order for ``--file1`` and ``--file2``. + + +Interleaved FASTQ reads +----------------------- + +AdapterRemoval is able to read and write paired-end reads stored in a single, so-called interleaved FASTQ file (one pair at a time, first mate 1, then mate 2). This is accomplished by specifying the location of the file using ``--file1`` and *also* setting the ``--interleaved`` command-line option:: + + AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved + +Other than taking just a single input file, this mode operates almost exactly like paired end trimming (as described above); the mode differs only in that paired reads are not written to a 'pair1' and a 'pair2' file, but instead these are instead written to a single, interleaved file, named 'paired'. The location of this file is controlled using the ``--output1`` option. Enabling either reading or writing of interleaved FASTQ files, both not both, can be accomplished by specifying the either of the ``--interleaved-input`` and ``--interleaved-output`` options, both of which are enabled by the ``--interleaved`` option. + + +Combining FASTQ output +---------------------- + +By default, AdapterRemoval will create one output file for each mate, one file for discarded reads, and (in PE mode) one file paired reads where one mate has been discarded, and (optionally) two files for collapsed reads. Alternatively, these files may be combined using the ``--combined-output``, in which case all output is directed to the mate 1 and (in PE mode) to the mate 2 file. In cases where reads are discarded due to trimming to due to being collapsed into a single sequence, the sequence and quality scores of the discarded read is replaced with a single 'N' with base-quality 0. This option may be combined with ``--interleaved`` / ``--interleaved-output``, to write a single, interleaved file in paired-end mode. + + +Different quality score encodings +--------------------------------- + +By default, AdapterRemoval expects the quality scores in FASTQ reads to be Phred+33 encoded, meaning that the error probabilities are encoded as (char)('!' - 10 * log10(p)). Most data will be encoded using Phred+33, but Phred+64 and 'Solexa' encoded quality scores are also supported. These are selected by specifying the ``--qualitybase`` command-line option (specifying either '33', '64', or 'solexa'):: + + AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename output_phred_64 + +By default, reads are written using the *same* encoding as the input. If a different encoding is desired, this may be accomplished using the ``--qualitybase-output`` option:: + + AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename output_phred_33 + +Note furthermore that AdapterRemoval by default only expects quality scores in the range 0 - 41 (or -5 to 41 in the case of Solexa encoded scores). If input data using a different maximum quality score is to be processed, or if the desired maximum quality score of collapsed reads is greater than 41, then this limit may be increased using the ``--qualitymax`` option:: + + AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapse --basename output_collapsed_q50 + +For a detailed overview of Phred encoding schemes currently and previously in use, see e.g. the Wikipedia article on the subject: +https://en.wikipedia.org/wiki/FASTQ_format#Encoding + + +Trimming paired-end reads with multiple adapter pairs +----------------------------------------------------- + +It is possible to trim data that contains multiple adapter pairs, by providing a one or two-column table containing possible adapter combinations (for single-end and paired-end trimming, respectively; see e.g. examples/adapters.txt):: + + cat adapters.txt + AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + AAACTTGCTCTGTGCCCGCTCCGTATGTCACAACAGTGCGTGTATCACCTCAATGCAGGACTCA GATCGGGAGTAATTTGGAGGCAGTAGTTCGTCGAAACTCGGAGCGTCTTTAGCAGGAG + CTAATTTGCCGTAGCGACGTACTTCAGCCTCCAGGAATTGGACCCTTACGCACACGCATTCATG TACCGTGAAAGGTGCGCTTAGTGGCATATGCGTTAAGAGCTAGGTAACGGTCTGGAGG + GTTCATACGACGACGACCAATGGCACACTTATCCGGTACTTGCGTTTCAATGCGCATGCCCCAT TAAGAAACTCGGAGTTTGGCCTGCGAGGTAGCTTGGGTGTTATGAAGAACGGCATGCG + CCATGCCCCGAAGATTCCTATACCCTTAAGGTCGCAATTGTTCGAGTAAGCTGTACGCGCCCAT GTTGCATTGACCCGAAGGGCTCGATGTTTAGGGAGGTCAGAAGTTGAGCGGGTTCAAA + +This table is then specified using the ``--adapter-list`` option:: + + AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt + +The resulting .summary file contains an overview of how frequently each adapter (pair) was used. + +Note that in the case of paired-end adapters, AdapterRemoval considers only the combinations of adapters specified in the table, one combination per row. For single-end trimming, only the first column of the table file is required, and the list may therefore take the form of a file containing one sequence per line. + + +Identifying adapter sequences from paired-ended reads +----------------------------------------------------- + +If we did not know the adapter sequences for the *reads_*.fq* files, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adapter sequence (not counting differences in index sequences). + +In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the ``--adapter1`` or ``--adapter2`` command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA:: + + AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq + + Attemping to identify adapter sequences ... + Processed a total of 1,000 reads in 0.0s; 129,000 reads per second on average ... + Found 394 overlapping pairs ... + Of which 119 contained adapter sequence(s) ... + + Printing adapter sequences, including poly-A tails: + --adapter1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG + ||||||||||||||||||||||||||||||||||******|||||||||||||||||||||||| + Consensus: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAA + Quality: 55200522544444/4411330333330222222/1.1.1.1111100-00000///..+....--*-)),,+++++++**(('%%%$ + + Top 5 most common 9-bp 5'-kmers: + 1: AGATCGGAA = 96.00% (96) + 2: AGATGGGAA = 1.00% (1) + 3: AGCTCGGAA = 1.00% (1) + 4: AGAGCGAAA = 1.00% (1) + 5: AGATCGGGA = 1.00% (1) + + + --adapter2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + Consensus: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + Quality: 525555555144141441430333303.2/22-2/-1..11111110--00000///..+....--*-),,,+++++++**(%'%%%$ + + Top 5 most common 9-bp 5'-kmers: + 1: AGATCGGAA = 100.00% (100) + +No files are generated from running the adapter identification step. + +The consensus sequences inferred are compared to those specified using the ``--adapter1`` and ``--adapter2`` command-line options, or with the default values for these if no values have been given (as in this case). Pipes (|) indicate matches between the provided sequences and the consensus sequence, and "*" indicate the presence of unspecified bases (Ns). + + +Demultiplexing and adapter-trimming +----------------------------------- + +As of version 2.1, AdapterRemoval supports simultaneous demultiplexing and adapter trimming; demultiplexing is carried out using a simple comparison between the specified barcode (a sequence of A, C, G, and T) and the first N bases of the mate 1 read, where N is the length of the barcode. Demultiplexing of double-indexed sequences is also supported, in which case two barcodes must be specified for each sample. The first barcode is then compared to first N_1 bases of the mate 1 read, and the second barcode is compared to the first N_2 bases of the mate 2 read. By default, this comparison requires a perfect match. Reads identified as containing a specific barcode(s) are then trimmed using adapter sequences including the barcode(s) as necessary. Reads for which no (pair of) barcodes matched are written to a separate file or pair of files (for paired end reads). + +Demultiplexing is enabled by creating a table of barcodes, the first column of which species the sample name (using characters a-z, A-Z, 0-9, or _) and the second and (optional) third columns specifies the barcode sequences expected at the 5' termini of mate 1 and mate 2 reads, respectively. + +For example, a table of barcodes from a double-indexed run might be as follows (see examples/barcodes.txt):: + + cat barcodes.txt + sample_1 ATGCGGA TGAATCT + sample_2 ATGGATT ATAGTGA + sample_7 CAAAACT TCGCTGC + +In the case of single-read reads, only the first two columns are required. AdapterRemoval is invoked with the ``--barcode-list`` option, specifying the path to this table:: + + AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_demux --barcode-list barcodes.txt + +This generates a set of output files for each sample specified in the barcode table, using the basename (``--basename``) as the prefix, followed by a dot and the sample name, followed by a dot and the default name for a given file type. For example, the output files for sample_2 would be + + * output_demux.sample_2.discarded + * output_demux.sample_2.pair1.truncated + * output_demux.sample_2.pair2.truncated + * output_demux.sample_2.settings + * output_demux.sample_2.singleton.truncated + +The settings files generated for each sample summarizes the reads for that sample only; in addition, a basename.settings file is generated which summarizes the number and proportion of reads identified as belonging to each sample. + +The maximum number of mismatches allowed when comparing barocdes is controlled using the options ``--barcode-mm``, ``--barcode-mm-r1``, and ``--barcode-mm-r2``, which specify the maximum number of mismatches total, and the maximum number of mismatches for the mate 1 and mate 2 barcodes respectively. Thus, if mm_1(i) and mm_2(i) represents the number of mismatches observed for barcode-pair i for a given pair of reads, these options require that + + 1. mm_1(i) <= ``--barcode-mm-r1`` + 2. mm_2(i) <= ``--barcode-mm-r2`` + 3. mm_1(i) + mm_2(i) <= ``--barcode-mm`` + + +Demultiplexing mode +------------------- + +As of version 2.2, AdapterRemoval can furthermore be used to demultiplex reads, without carrying out other forms of adapter trimming. This is accomplished by specifying the ``--demultiplex-only`` option: + + AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_only_demux --barcode-list barcodes.txt --demultiplex-only + +Options listed under "TRIMMING SETTINGS" (see *AdapterRemoval --help*) do not apply to this mode, but compression (``--gzip``, ``--bzip2``), multi-threading (``--threads``), interleaving (``--interleaved``, etc.) and other such options may be used in conjunction with ``--demultiplex-only``. + +AdapterRemoval will generate a *.settings* file for each sample listed in the ``--barcode-list`` file, along with the adapter-sequences that should be used when trimming reads for a given sample. These adapters correspond to the adapters that were specified when running AdapterRemoval in demultiplexing mode, with the barcode prefixed as appropriate. An underscore is used to demarcate the location at which the barcode ends and the adapter beings. + +It is important to use these, updated, adapter sequences when trimming the demultiplexed reads, to avoid the inclusion of barcode sequences in reads extending past the 3' termini of the DNA template sequence. diff -Nru adapterremoval-2.2.2/docs/getting_started.rst adapterremoval-2.2.3/docs/getting_started.rst --- adapterremoval-2.2.2/docs/getting_started.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/getting_started.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,43 @@ +.. highlight:: Bash + +Getting started +=============== + +To run AdapterRemoval on single-end FASTQ data, simply specify the location of FASTQ file(s) using the ``--file1`` command-line options:: + + AdapterRemoval --file1 myreads_1.fastq.gz + +To run AdapterRemoval on paired-end FASTQ data, specify the location of the mate 1 and mate 2 FASTQ files using the ``--file1`` and ``--file2`` command-line options:: + + AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz + +The files may be uncompressed, gzip-compressed, or bzip2 compressed. When run in this manner, AdapterRemoval will save the trimmed reads in the current working directly, using filenames starting with 'your_output'. This behavior may be changed using the ``--basename`` option, or using specific options for each output file. See the :doc:`input_and_output` section for more information about files generated by AdapterRemoval. + +More examples of common usage may be found in the :doc:`examples` section of the documentation. + + +A note on specifying adapters +----------------------------- + +AdapterRemoval relies on the user specifying the adapter sequences to be trimmed, using the ``--adapter1`` and ``--adapter2`` command-line options. By default, AdapterRemoval is setup to trim Illumina Truseq adapters, corresponding to the following command-line options:: + + --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG + --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + +It is therefore extremely important to specify the correct adapter sequences when running AdapterRemoval on a dataset that does not make use of these adapters. Failure to do so will result in the wrong sequences being trimmed, and actual adapter sequences being left in the resulting "trimmed" reads. + +Adapter sequences are specified in the read orientation when using the ``--adapter1`` and ``--adapter2`` command-line options, directly corresponding to the sequence that is observed in the FASTQ files produced by the base calling software. If we were processing data generated using the above TrueSeq adapters, then we would therefore expect to find those sequences as-is in our FASTQ files (assuming that the read lengths are sufficiently long and that insert sizes are sufficiently short), typically followed by a low-quality A-tail:: + + $ grep "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC......ATCTCGTATGCCGTCTTCTGCTTG" file1.fq + AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAACAAGAAT + CTGGAGTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA + GGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGAATCTCGTATGCCGTCTTCTGCTTGCAAATTGAAAACAC + + $ grep "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" file2.fq + CAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAGAAAAACATCTTG + GAACTCCAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAAAAATAGA + GAACTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTCAAAAACATAAGACCTA + +The ambiguous bases representing the mate 1 barcode (the six Ns) have been replaced by single-character wildcards (dots) in the above grep commands, corresponding to how AdapterRemoval itself treats such characters. + +For paired-end data, the ``--identify-adapters`` mode may be used to verify the choice of adapters, by attempting to reconstruct the adapter sequence directly from the FASTQ reads. See the :doc:`examples` section for a demonstration of this functionality. diff -Nru adapterremoval-2.2.2/docs/index.rst adapterremoval-2.2.3/docs/index.rst --- adapterremoval-2.2.2/docs/index.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/index.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,33 @@ +AdapterRemoval +============== + +AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. + +If you use AdapterRemoval v2, then please cite the paper: + + Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 + http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 + +AdapterRemoval was originally published in Lindgreen 2012: + + Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation Sequencing Reads, BMC Research Notes, 5:337 + http://www.biomedcentral.com/1756-0500/5/337/ + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + installation + getting_started + examples + manpage + misc + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff -Nru adapterremoval-2.2.2/docs/input_and_output.rst adapterremoval-2.2.3/docs/input_and_output.rst --- adapterremoval-2.2.2/docs/input_and_output.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/input_and_output.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +Input and output files +====================== + + +Output files +------------ diff -Nru adapterremoval-2.2.2/docs/installation.rst adapterremoval-2.2.3/docs/installation.rst --- adapterremoval-2.2.2/docs/installation.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/installation.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +.. highlight:: Bash + +Installation +============ + +Installing on Debian based systems +---------------------------------- + +Debian users on Stretch, Buster, or Sid, or using Jessie-backports, as well as Ubuntu users on Zesty or Artful, may install AdapterRemoval using apt:: + + apt-get install adapterremoval + +For other distributions, or to get the latest version of AdapteRemoval, please see the `Installing from sources`_ section below. + + +Installing on OSX +----------------- + +MacOSX users may install AdapterRemoval using Homebrew:: + + brew install homebrew/science/adapterremoval + +Please see the Homebrew website for instructions on how to install and use Homebrew: + + https://brew.sh/ + + +Installing from sources +----------------------- + +Installing AdapterRemoval from sources requires the presence of libz and bz2 headers. On Debian based systems, these may be installed as follows:: + + sudo apt-get install zlib1g-dev libbz2-dev + +In addtion, a C++11 compatible compiler and basic build-tools are required. On Debian based systems, these may be installed as follows:: + + sudo apt-get install build-essential + +To compile AdapterRemoval, first download and unpack the newest release from GitHub, and then run the 'make' command:: + + wget -O adapterremoval-2.2.2.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v2.2.2.tar.gz + tar xvzf adapterremoval-2.2.2.tar.gz + cd adapterremoval-2.2.2 + make + +The resulting 'AdapterRemoval' executable is located in the 'build' subdirectory, and can be run as-is. It is also possible to perform a system-wide installation of the AdapterRemoval executable, man-page, and examples using the following command:: + + sudo make install diff -Nru adapterremoval-2.2.2/docs/manpage.rst adapterremoval-2.2.3/docs/manpage.rst --- adapterremoval-2.2.2/docs/manpage.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/manpage.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,297 @@ +AdapterRemoval manpage +====================== + +Synopsis +-------- + +**AdapterRemoval** [*options*...] --file1 <*filenames*> [--file2 <*filenames*>] + + +Description +----------- + +:program:`AdapterRemoval` removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads, optionally trimming Ns and low qualities bases and/or collapsing overlapping paired-end mates into one read. Low quality reads are filtered based on the resulting length and the number of ambigious nucleotides ('N') present following trimming. These operations may be combined with simultaneous demultiplexing using 5' barcode sequences. Alternatively, ``AdapterRemoval`` may attempt to reconstruct a consensus adapter sequences from paired-end data, in order to allow the identification of the adapter sequences originally used. + +If you use this program, please cite the paper: + + Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 + + http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 + + +For detailed documentation, please see + + http://adapterremoval.readthedocs.io/en/v2.2.3/ + + +Options +------- + +.. program:: AdapterRemoval + +.. option:: --help + + Display summary of command-line options. + +.. option:: --version + + Print the version string. + +.. option:: --file1 filename [filenames...] + + Read FASTQ reads from one or more files, either uncompressed, bzip2 compressed, or gzip compressed. This contains either the single-end (SE) reads or, if paired-end, the mate 1 reads. If running in paired-end mode, both ``--file1`` and ``--file2`` must be set. See the primary documentation for a list of supported formats. + +.. option:: --file2 filename [filenames...] + + Read one or more FASTQ files containing mate 2 reads for a paired-end run. If specified, ``--file1`` must also be set. + +.. option:: --identify-adapters + + Attempt to build a consensus adapter sequence from fully overlapping pairs of paired-end reads. The minimum overlap is controlled by ``--minalignmentlength``. The result will be compared with the values set using ``--adapter1`` and ``--adapter2``. No trimming is performed in this mode. Default is off. + +.. option:: --threads n + + Maximum number of threads. Defaults to 1. + + +FASTQ options +~~~~~~~~~~~~~ +.. option:: --qualitybase base + + The Phred quality scores encoding used in input reads - either '64' for Phred+64 (Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. Default is 33. + +.. option:: --qualitybase-output base + + The base of the quality score for reads written by AdapterRemoval - either '64' for Phred+64 (i.e., Illumina 1.3+ and 1.5+) or '33' for Phred+33 (Illumina 1.8+). In addition, the value 'solexa' may be used to specify reads with Solexa encoded scores. However, note that quality scores are represented using Phred scores internally, and conversion to and from Solexa scores therefore result in a loss of information. The default corresponds to the value given for ``--qualitybase``. + +.. option:: --qualitymax base + + Specifies the maximum Phred score expected in input files, and used when writing output files. Possible values are 0 to 93 for Phred+33 encoded files, and 0 to 62 for Phred+64 encoded files. Defaults to 41. + +.. option:: --mate-separator separator + + Character separating the mate number (1 or 2) from the read name in FASTQ records. Defaults to '/'. + +.. option:: --interleaved + + Enables ``--interleaved-input`` and ``--interleaved-output``. + +.. option:: --interleaved-input + + If set, input is expected to be a interleaved FASTQ files specified using ``--file1``, in which pairs of reads are written one after the other (e.g. read1/1, read1/2, read2/1, read2/2, etc.). + +.. option:: --interleaved-ouput + + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads. By default, this file is named ``basename.paired.truncated``, but this may be changed using the ``--output1`` option. + +.. option:: --combined-output + + Write all reads into the files specified by ``--output1`` and ``--output2``. The sequences of reads discarded due to quality filters or read merging are replaced with a single 'N' with Phred score 0. This option can be combined with ``--interleaved-output`` to write PE reads to a single output file specified with ``--output1``. + + +Output file options +~~~~~~~~~~~~~~~~~~~ +.. option:: --basename filename + + Prefix used for the naming output files, unless these names have been overridden using the corresponding command-line option (see below). + +.. option:: --settings file + + Output file containing information on the parameters used in the run as well as overall statistics on the reads after trimming. Default filename is 'basename.settings'. + +.. option:: --output1 file + + Output file containing trimmed mate1 reads. Default filename is 'basename.pair1.truncated' for paired-end reads, 'basename.truncated' for single-end reads, and 'basename.paired.truncated' for interleaved paired-end reads. + +.. option:: --output2 file + + Output file containing trimmed mate 2 reads when ``--interleaved-output`` is not enabled. Default filename is 'basename.pair2.truncated' in paired-end mode. + +.. option:: --singleton file + + Output file to which containing paired reads for which the mate has been discarded. Default filename is 'basename.singleton.truncated'. + +.. option:: --outputcollapsed file + + If --collapsed is set, contains overlapping mate-pairs which have been merged into a single read (PE mode) or reads for which the adapter was identified by a minimum overlap, indicating that the entire template molecule is present. This does not include which have subsequently been trimmed due to low-quality or ambiguous nucleotides. Default filename is 'basename.collapsed' + +.. option:: --outputcollapsedtruncated file + + Collapsed reads (see --outputcollapsed) which were trimmed due the presence of low-quality or ambiguous nucleotides. Default filename is 'basename.collapsed.truncated'. + +.. option:: --discarded file + + Contains reads discarded due to the --minlength, --maxlength or --maxns options. Default filename is 'basename.discarded'. + + +Output compression options +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. option:: --gzip + + If set, all FASTQ files written by AdapterRemoval will be gzip compressed using the compression level specified using ``--gzip-level``. The extension ".gz" is added to files for which no filename was given on the command-line. Defaults to off. + +.. option:: --gzip-level level + + Determines the compression level used when gzip'ing FASTQ files. Must be a value in the range 0 to 9, with 0 disabling compression and 9 being the best compression. Defaults to 6. + +.. option:: --bzip2 + + If set, all FASTQ files written by AdapterRemoval will be bzip2 compressed using the compression level specified using ``--bzip2-level``. The extension ".bz2" is added to files for which no filename was given on the command-line. Defaults to off. + +.. option:: --bzip2-level level + + Determines the compression level used when bzip2'ing FASTQ files. Must be a value in the range 1 to 9, with 9 being the best compression. Defaults to 9. + + +FASTQ trimming options +~~~~~~~~~~~~~~~~~~~~~~ + +.. option:: --adapter1 adapter + + Adapter sequence expected to be found in mate 1 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the "Adapters" section of the online documentation. Default is AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG. + +.. option:: --adapter2 adapter + + Adapter sequence expected to be found in mate 2 reads, specified in read direction. For a detailed description of how to provide the appropriate adapter sequences, see the "Adapters" section of the online documentation. Default is AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT. + +.. option:: --adapter-list filename + + Read one or more adapter sequences from a table. The first two columns (separated by whitespace) of each line in the file are expected to correspond to values passed to --adapter1 and --adapter2. In single-end mode, only column one is required. Lines starting with '#' are ignored. When multiple rows are found in the table, AdapterRemoval will try each adapter (pair), and select the best aligning adapters for each FASTQ read processed. + +.. option:: --minadapteroverlap length + + In single-end mode, reads are only trimmed if the overlap between read and the adapter is at least X bases long, not counting ambiguous nucleotides (N); this is independent of the ``--minalignmentlength`` when using ``--collapse``, allowing a conservative selection of putative complete inserts in single-end mode, while ensuring that all possible adapter contamination is trimmed. The default is 0. + +.. option:: --mm mismatchrate + + The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If ```--mismatchrate`` is greater than 1, the rate is set to 1 / ``--mismatchrate``. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using ``--identify-adapters``. + +.. option:: --shift n + + To allow for missing bases in the 5' end of the read, the program can let the alignment slip ``--shift`` bases in the 5' end. This corresponds to starting the alignment maximum ``--shift`` nucleotides into read2 (for paired-end) or the adapter (for single-end). The default is 2. + +.. option:: --trim5p n [n] + + Trim the 5' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts. Off by default. + +.. option:: --trim3p n [n] + + Trim the 3' of reads by a fixed amount. See ``--trim5p``. + +.. option:: --trimns + + Trim consecutive Ns from the 5' and 3' termini. If quality trimming is also enabled (``--trimqualities``), then stretches of mixed low-quality bases and/or Ns are trimmed. + +.. option:: --maxns n + + Discard reads containing more than ``--max`` ambiguous bases ('N') after trimming. Default is 1000. + +.. option:: --trimqualities + + Trim consecutive stretches of low quality bases (threshold set by ``--minquality``) from the 5' and 3' termini. If trimming of Ns is also enabled (``--trimns``), then stretches of mixed low-quality bases and Ns are trimmed. + +.. option:: --trimwindows window_size + + Trim low quality bases using a sliding window based approach inspired by :program:`sickle` with the given window size. See the "Window based quality trimming" section of the manual page for a description of this algorithm. + +.. option:: --minquality minimum + + Set the threshold for trimming low quality bases using ``--trimqualities`` and ``--trimwindows``. Default is 2. + +.. option:: --minlength length + + Reads shorter than this length are discarded following trimming. Defaults to 15. + +.. option:: --maxlength length + + Reads longer than this length are discarded following trimming. Defaults to 4294967295. + + + +FASTQ merging options +~~~~~~~~~~~~~~~~~~~~~ + +.. option:: --collapse + + In paired-end mode, merge overlapping mates into a single and recalculate the quality scores. In single-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete "collapsed" reads are written with a 'M\_' name prefix, and "collapsed" reads which are trimmed due to quality settings are written with a 'MT\_' name prefix. The overlap needs to be at least ``--minalignmentlength`` nucleotides, with a maximum number of mismatches determined by ``--mm``. + +.. option:: --minalignmentlength length + + The minimum overlap between mate 1 and mate 2 before the reads are collapsed into one, when collapsing paired-end reads, or when attempting to identify complete template sequences in single-end mode. Default is 11. + +.. option:: --seed seed + + When collaping reads at positions where the two reads differ, and the quality of the bases are identical, AdapterRemoval will select a random base. This option specifies the seed used for the random number generator used by AdapterRemoval. This value is also written to the settings file. Note that setting the seed is not reliable in multithreaded mode, since the order of operations is non-deterministic. + +.. option:: --deterministic + + Enable deterministic mode; currently only affects --collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. + + +FASTQ demultiplexing options +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. option:: --barcode-list filename + + Perform demultiplxing using table of one or two fixed-length barcodes for SE or PE reads. The table is expected to contain 2 or 3 columns, the first of which represent the name of a given sample, and the second and third of which represent the mate 1 and (optionally) the mate 2 barcode sequence. For a detailed description, see the "Demultiplexing" section of the online documentation. + +.. option:: --barcode-mm n + Maximum number of mismatches allowed when counting mismatches in both the mate 1 and the mate 2 barcode for paired reads. + +.. option:: --barcode-mm-r1 n + + Maximum number of mismatches allowed for the mate 1 barcode; if not set, this value is equal to the ``--barcode-mm`` value; cannot be higher than the ``--barcode-mm`` value. + +.. option:: --barcode-mm-r2 n + + Maximum number of mismatches allowed for the mate 2 barcode; if not set, this value is equal to the ``--barcode-mm`` value; cannot be higher than the ``--barcode-mm`` value. + +.. option:: --demultiplex-only + + Only carry out demultiplexing using the list of barcodes supplied with --barcode-list. No other processing is done. + + +Window based quality trimming +----------------------------- + +As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base-trimming inspired by ``sickle``. If ``window_size`` is greater than or equal to 1, that number is used as the window size for all reads. If ``window_size`` is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. + +Reads are trimmed as follows for a given window size: + + 1. The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than ``--minquality``. + + 2. The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to ``--minquality``. The new 3' is placed at the last base in that window where the quality is greater than or equal to ``--minquality``. + + 3. If no 5' position could be determined, the read is discarded. + + +Exit status +----------- + +AdapterRemoval exists with status 0 if the program ran succesfully, and with a non-zero exit code if any errors were encountered. Do not use the output from AdapterRemoval if the program returned a non-zero exit code! + + +Reporting bugs +-------------- + +Please report any bugs using the AdapterRemoval issue-tracker: + +https://github.com/MikkelSchubert/adapterremoval/issues + + +License +------- + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 3 of the License, or +at your option any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . diff -Nru adapterremoval-2.2.2/docs/misc.rst adapterremoval-2.2.3/docs/misc.rst --- adapterremoval-2.2.2/docs/misc.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/misc.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,35 @@ +Miscellaneous +============= + + +Window-based quality trimming +----------------------------- + +As of v2.2.2, AdapterRemoval implements sliding window based approach to quality based base-trimming inspired by `sickle`_. If ``window_size`` is greater than or equal to 1, that number is used as the window size for all reads. If ``window_size`` is a number greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. + +Reads are trimmed as follows for a given window size: + + 1. The new 5' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than ``--minquality``. + + 2. The new 3' is located by sliding the first window right, until the average quality becomes less than or equal to ``--minquality``. The new 3' is placed at the last base in that window where the quality is greater than or equal to ``--minquality``. + + 3. If no 5' position could be determined, the read is discarded. + + +Migrating from AdapterRemoval v1.x +---------------------------------- + +Command-line options mostly behave the same between AdapterRemoval v1 and AdapterRemoval v2, and scripts written with AdapterRemoval v1.x in mind should work with AdapterRemoval v2.x. A notable exception is the ``--pcr1`` and ``--pcr2`` options, which have been replaced by the ``--adapter1`` and ``--adapter2`` options described above. While the ``--pcr`` options are still supported for backwards compatibility, these should not be used going forward. + +The difference between these two options is that ``--adapter2`` expects the mate 2 adapter sequence to be specified in the read orientation as described above, while the ``--pcr2`` expects the sequence to be in the same orientation as the mate 1 sequence, the reverse complement of the sequence observed in the mate 2 reads. + +Using the common 13 bp Illumina adapter sequence (AGATCGGAAGAGC) as an example, this is how the options would be used in AdapterRemoval v2.x:: + + AdapterRemoval --adapter1 AGATCGGAAGAGC --adapter2 AGATCGGAAGAGC ... + +And in AdapterRemoval v1.x:: + + AdapterRemoval --adapter1 AGATCGGAAGAGC --adapter2 GCTCTTCCGATCT ... + + +.. _sickle: https://github.com/najoshi/sickle \ No newline at end of file diff -Nru adapterremoval-2.2.2/docs/README.rst adapterremoval-2.2.3/docs/README.rst --- adapterremoval-2.2.2/docs/README.rst 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/docs/README.rst 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,107 @@ +AdapterRemoval v2 +================= + +.. image:: https://img.shields.io/travis/MikkelSchubert/adapterremoval/master.svg + :target: https://travis-ci.org/MikkelSchubert/adapterremoval + :alt: Travis-CI + +.. image:: https://img.shields.io/coveralls/MikkelSchubert/adapterremoval.svg + :target: https://coveralls.io/github/MikkelSchubert/adapterremoval + :alt: Coveralls + +AdapterRemoval searches for and removes adapter sequences from High-Throughput +Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end +of reads following adapter removal. AdapterRemoval can analyze both single end +and paired end data, and can be used to merge overlapping paired-ended reads +into (longer) consensus sequences. Additionally, AdapterRemoval can construct a +consensus adapter sequence for paired-ended reads, if which this information is +not available. + +If you use AdapterRemoval v2, then please cite the paper + + Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter + trimming, identification, and read merging. BMC Research Notes, 12;9(1):88 + http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2 + +AdapterRemoval was originally published in Lindgreen 2012: + + Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation + Sequencing Reads, BMC Research Notes, 5:337 + http://www.biomedcentral.com/1756-0500/5/337/ + + +Overview of major features +========================== + + - Trimming of adapters sequences from single-end and paired-end FASTQ reads. + - Trimming of multiple, different adapters or adapter pairs. + - Demultiplexing of single or double indexed reads, with or without trimming + of adapter sequences. + - Reconstruction of adapter sequences from paired-end reads, by the pairwise + alignment of reads in the absence of a known adapter sequence. + - Merging of overlapping read-pairs into higher-quality consensus sequences. + - Multi-threading of all operations for increased throughput. + - Reading and writing of gzip and bzip2 compressed files. + - Reading and writing of interleaved FASTQ files. + + +Installation +============ + +For detailed installation instructions, please see the +`Installation `_ +section of the online documentation. + +Installing AdapterRemoval using `Conda `_ +----------------------------------------------------------------- + +If you have Conda `installed on your system `_, +you may install AdapterRemoval using one of serveral unoffical recipies:: + + conda install -c bioconda adapterremoval + conda install -c maxibor adapterremoval2 + + +Installing AdapterRemoval on Debian based systems +------------------------------------------------- + +Users of Debian Stretch or Ubuntu Artful Aardvark may install AdapterRemoval +using Apt:: + + sudo apt-get install adapterremoval adapterremoval-examples + + +Building AdapterRemoval from scratch +------------------------------------ + +Compiling AdapterRemoval from scratch requires a C++11 compliant compiler, and +that the zlib and bz2lib headers are installed:: + + make + sudo make install + + +Getting started +=============== + +To run AdapterRemoval, specify the location of pair 1 and (optionally) pair 2 +FASTQ using the --file1 and --file2 command-line options:: + + AdapterRemoval --file1 myreads_1.fastq.gz --file2 myreads_2.fastq.gz + +By default, AdapterRemoval will save the trimmed reads in the current working +directly, using filenames starting with 'your_output'. See the +`Input and Output +`_ +files section for more information about files generated by AdapterRemoval. + +More examples of common usage may be found in the +`Examples `_ +section of the online documentation. + + +Documentation +------------- + +For a detailed description of program usage, please refer to the online +`online documentation `_. diff -Nru adapterremoval-2.2.2/Makefile adapterremoval-2.2.3/Makefile --- adapterremoval-2.2.2/Makefile 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/Makefile 2019-01-22 21:39:48.000000000 +0000 @@ -86,21 +86,21 @@ DFILES := $(OBJS:.o=.deps) -.PHONY: all install clean test clean_tests static validate validation +.PHONY: all install clean test clean_tests static regression docs -all: build/$(PROG) build/$(PROG).1 +all: build/$(PROG) -everything: all static test validation +everything: all static test regression docs # Clean -clean: clean_tests +clean: clean_tests clean_docs @echo $(COLOR_GREEN)"Cleaning ..."$(COLOR_END) - $(QUIET) rm -f build/$(PROG) build/$(PROG).1 build/$(LIBNAME).a - $(QUIET) rm -rvf build/validation + $(QUIET) rm -f build/$(PROG) build/$(LIBNAME).a + $(QUIET) rm -rvf build/regression $(QUIET) rm -rvf $(BDIR) # Install -install: build/$(PROG) build/$(PROG).1 +install: build/$(PROG) @echo $(COLOR_GREEN)"Installing AdapterRemoval .."$(COLOR_END) @echo $(COLOR_GREEN)" .. binary into ${PREFIX}/bin/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/bin/ @@ -109,7 +109,7 @@ @echo $(COLOR_GREEN)" .. man-page into ${PREFIX}/share/man/man1/"$(COLOR_END) $(QUIET) mkdir -p ${PREFIX}/share/man/man1/ - $(QUIET) mv -f build/$(PROG).1 ${PREFIX}/share/man/man1/ + $(QUIET) cp -a $(PROG).1 ${PREFIX}/share/man/man1/ $(QUIET) chmod a+r ${PREFIX}/share/man/man1/$(PROG).1 @echo $(COLOR_GREEN)" .. README into ${PREFIX}/share/adapterremoval/"$(COLOR_END) @@ -141,11 +141,6 @@ @echo $(COLOR_GREEN)"Linking static library $@"$(COLOR_END) $(AR) rcs build/$(LIBNAME).a $(LIBOBJS) -build/%.1: %.pod - @echo $(COLOR_GREEN)"Constructing man-page $@ from $<"$(COLOR_END) - $(QUIET) mkdir -p $(BDIR) - $(QUIET) pod2man $< > $@ - # Automatic header depencencies -include $(DFILES) @@ -154,11 +149,12 @@ # Unit testing # TEST_DIR := build/tests -TEST_OBJS := $(TEST_DIR)/alignment.o \ +TEST_OBJS := $(TEST_DIR)/main_test.o \ + $(TEST_DIR)/debug.o \ + $(TEST_DIR)/alignment.o \ $(TEST_DIR)/alignment_test.o \ $(TEST_DIR)/argparse.o \ $(TEST_DIR)/argparse_test.o \ - $(TEST_DIR)/debug.o \ $(TEST_DIR)/fastq.o \ $(TEST_DIR)/fastq_test.o \ $(TEST_DIR)/fastq_enc.o \ @@ -167,30 +163,21 @@ $(TEST_DIR)/strutils_test.o TEST_DEPS := $(TEST_OBJS:.o=.deps) -GTEST_DIR := googletest-release-1.8.0/googletest -GTEST_OBJS := $(TEST_DIR)/gtest-all.o $(TEST_DIR)/gtest_main.o -GTEST_LIB := $(TEST_DIR)/libgtest.a - -TEST_CXXFLAGS := -isystem $(GTEST_DIR)/include -I$(GTEST_DIR) -Isrc -DAR_TEST_BUILD -g -GTEST_CXXFLAGS := $(TEST_CXXFLAGS) +TEST_CXXFLAGS := -Isrc -DAR_TEST_BUILD -g test: $(TEST_DIR)/main - @echo $(COLOR_GREEN)"Running tests"$(COLOR_END) - $(QUIET) $< --gtest_print_time=0 --gtest_shuffle + @echo $(COLOR_GREEN)"Running unit tests"$(COLOR_END) + $(QUIET) $(TEST_DIR)/main clean_tests: @echo $(COLOR_GREEN)"Cleaning tests ..."$(COLOR_END) $(QUIET) rm -rvf $(TEST_DIR) -$(TEST_DIR)/main: $(GTEST_LIB) $(TEST_OBJS) +$(TEST_DIR)/main: $(TEST_OBJS) @echo $(COLOR_GREEN)"Linking executable $@"$(COLOR_END) $(QUIET) $(CXX) $(CXXFLAGS) ${LIBRARIES} $^ -o $@ -$(TEST_DIR)/libgtest.a: $(GTEST_OBJS) - @echo $(COLOR_GREEN)"Linking GTest library $@"$(COLOR_END) - $(QUIET) ar -rv $@ $^ - -$(TEST_DIR)/%.o: tests/%.cpp +$(TEST_DIR)/%.o: tests/unit/%.cpp @echo $(COLOR_CYAN)"Building $@ from $<"$(COLOR_END) $(QUIET) mkdir -p $(TEST_DIR) $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -c -o $@ $< @@ -202,47 +189,34 @@ $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -c -o $@ $< $(QUIET) $(CXX) $(CXXFLAGS) $(TEST_CXXFLAGS) -w -MM -MT $@ -MF $(@:.o=.deps) $< -$(TEST_DIR)/gtest%.o: $(GTEST_DIR)/src/gtest%.cc - @echo $(COLOR_CYAN)"Building $@ from $<"$(COLOR_END) - $(QUIET) mkdir -p $(TEST_DIR) - $(QUIET) $(CXX) $(GTEST_CXXFLAGS) -c $< -o $@ - -.PRECIOUS: $(GTEST_DIR)/src/gtest%.cc -$(GTEST_DIR)/src/gtest%.cc: googletest-release-1.8.0.zip - $(QUIET) if ! test -e "$@"; \ - then \ - echo $(COLOR_CYAN)"Unpacking Google Test library"$(COLOR_END); \ - unzip -qo googletest-release-1.8.0.zip; \ - fi - -googletest-release-1.8.0.zip: -ifneq ("$(shell which wget)", "") - @echo $(COLOR_CYAN)"Fetching Google Test library using wget"$(COLOR_END) - $(QUIET) wget -q https://github.com/google/googletest/archive/release-1.8.0.zip -O googletest-release-1.8.0.zip -else ifneq ("$(shell which curl)", "") - @echo $(COLOR_CYAN)"Fetching Google Test library using curl"$(COLOR_END) - $(QUIET) curl -L https://github.com/google/googletest/archive/release-1.8.0.zip -o googletest-release-1.8.0.zip -else - @echo $(COLOR_YELLOW)"To run tests, first download and unpack GoogleTest 1.8.0 in this folder:"$(COLOR_END) - @echo $(COLOR_YELLOW)" $$ wget https://github.com/google/googletest/archive/release-1.8.0.zip -O googletest-release-1.8.0.zip"$(COLOR_END) - @echo $(COLOR_YELLOW)" $$ unzip googletest-release-1.8.0.zip"$(COLOR_END) - @exit 1 -endif - # # Validation # -VALIDATION_BDIR=build/validation -VALIDATION_SDIR=validation +VALIDATION_BDIR=./build/regression +VALIDATION_SDIR=./tests/regression -validate: build/$(PROG) - @echo $(COLOR_CYAN)"Validating AdapterRemoval results"$(COLOR_END) +regression: build/$(PROG) + @echo $(COLOR_GREEN)"Running regression tests"$(COLOR_END) @mkdir -p $(VALIDATION_BDIR) - @./validation/run $(VALIDATION_BDIR) $(VALIDATION_SDIR) - -validation: validate + @$(VALIDATION_SDIR)/run $(VALIDATION_BDIR) $(VALIDATION_SDIR) # Automatic header dependencies for tests -include $(TEST_DEPS) + + +# +# Documentation +# +SPHINXOPTS = -n -q +SPHINXBUILD = sphinx-build + +docs: + $(QUIET) @$(SPHINXBUILD) -M html docs build/docs $(SPHINXOPTS) + $(QUIET) @$(SPHINXBUILD) -M man docs build/docs $(SPHINXOPTS) + $(QUIET) cp -v "build/docs/man/AdapterRemoval.1" . + +clean_docs: + @echo $(COLOR_GREEN)"Cleaning documentation ..."$(COLOR_END) + $(QUIET) rm -rvf build/docs diff -Nru adapterremoval-2.2.2/README.md adapterremoval-2.2.3/README.md --- adapterremoval-2.2.2/README.md 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/README.md 2019-01-22 21:39:48.000000000 +0000 @@ -29,6 +29,16 @@ ## Installation +### Installation with [Conda](https://conda.io/docs/) + +If you have Conda [installed on your system](https://conda.io/miniconda.html): + +``` + conda install -c maxibor adapterremoval2 +``` + +### Manual installation + To install, first download and unpack the newest release from GitHub: $ wget -O adapterremoval-2.1.7.tar.gz https://github.com/MikkelSchubert/adapterremoval/archive/v2.1.7.tar.gz @@ -166,7 +176,7 @@ If we did not know the adapter sequences for the 'reads\_*.fq' files, AdapterRemoval may be used to generate a consensus adapter sequence based on fragments identified as belonging to the adapters through pairwise alignments of the reads, provided that the data set contains only a single adapter sequence (not counting differences in index sequences). -In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the --adapter1 or --adapter2 command-line options. The characters shown under each of the consensus sequences represented the phred-encoded fraction of bases identical to the consensus base, with adapter 1 containing the index CACCTA: +In the following example, the identified adapters corresponds to the default adapter sequences with a poly-A tail resulting from sequencing past the end of the insert + templates. It is not necessary to specify this tail when using the --adapter1 or --adapter2 command-line options. The characters shown under each of the consensus sequences represent the Phred-encoded fraction of bases that differ from the consensus base, such that a high Phred score indicates a strong consensus. In the examples below, adapter 1 is observed to contain the index CACCTA: $ AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq diff -Nru adapterremoval-2.2.2/src/adapterset.cpp adapterremoval-2.2.3/src/adapterset.cpp --- adapterremoval-2.2.2/src/adapterset.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/adapterset.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -327,6 +327,7 @@ if (row.second.size() > 1) { adapter_3p = row.second.at(1); + adapter_3p.reverse_complement(); } m_adapters.push_back(fastq_pair(adapter_5p, adapter_3p)); diff -Nru adapterremoval-2.2.2/src/alignment.cpp adapterremoval-2.2.3/src/alignment.cpp --- adapterremoval-2.2.2/src/alignment.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/alignment.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -242,7 +242,7 @@ const std::string& sequence2, const std::string& qualities1, const std::string& qualities2, - std::mt19937& rng) + std::mt19937* rng) { AR_DEBUG_ASSERT(sequence1.length() == sequence2.length() && sequence1.length() == qualities1.length() && @@ -271,11 +271,15 @@ collapsed_qual.at(i) = PHRED_OFFSET_33; } } else if (nt_1 != nt_2 && qual_1 == qual_2) { - const int shuffle = rng() & 1; - collapsed_seq.at(i) = shuffle ? nt_1 : nt_2; + if (rng) { + collapsed_seq.at(i) = ((*rng)() & 1) ? nt_1 : nt_2; - const phred_scores& new_scores = get_updated_phred_scores(qual_1, qual_2); - collapsed_qual.at(i) = new_scores.different_nts; + const phred_scores& new_scores = get_updated_phred_scores(qual_1, qual_2); + collapsed_qual.at(i) = new_scores.different_nts; + } else { + collapsed_seq.at(i) = 'N'; + collapsed_qual.at(i) = PHRED_OFFSET_33; + } } else { // Ensure that nt_1 / qual_1 always contains the preferred nt / score // This is an assumption of the g_updated_phred_scores cache. @@ -451,7 +455,7 @@ fastq collapse_paired_ended_sequences(const alignment_info& alignment, const fastq& read1, const fastq& read2, - std::mt19937& rng, + std::mt19937* rng, const char mate_sep) { if (alignment.offset > static_cast(read1.length())) { diff -Nru adapterremoval-2.2.2/src/alignment.hpp adapterremoval-2.2.3/src/alignment.hpp --- adapterremoval-2.2.2/src/alignment.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/alignment.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -183,6 +183,8 @@ * a random base is selected. In both cases, the quality score is updated to * reflect the lower quality implied by these observations. * + * If rng is null, different bases with the same quality are set to N and !. + * * @return A single FASTQ record representing the collapsed sequence. * * Note that the sequences are assumed to have been trimmed using the @@ -192,7 +194,7 @@ fastq collapse_paired_ended_sequences(const alignment_info& alignment, const fastq& read1, const fastq& read2, - std::mt19937& rng, + std::mt19937* rng, const char mate_sep=MATE_SEPARATOR); diff -Nru adapterremoval-2.2.2/src/argparse.cpp adapterremoval-2.2.3/src/argparse.cpp --- adapterremoval-2.2.2/src/argparse.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/argparse.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -113,6 +113,16 @@ parse_result parser::parse_args(int argc, char* argv[]) { const string_vec argvec(argv + 1, argv + argc); + for (const auto& arg : argvec) { + if (arg == "--help" || arg == "-h") { + print_help(); + return parse_result::exit; + } else if (arg == "--version") { + print_version(); + return parse_result::exit; + } + } + string_vec_citer it = argvec.begin(); while (it != argvec.end()) { consumer_map::iterator parser = m_parsers.end(); @@ -143,14 +153,6 @@ } } - if (is_set("--help")) { - print_help(); - return parse_result::exit; - } else if (is_set("--version")) { - print_version(); - return parse_result::exit; - } - return parse_result::ok; } @@ -202,33 +204,11 @@ void parser::print_arguments(const key_pair_vec& keys) const { - size_t indentation = 0; - for (const auto& key_pair : keys) { - if (key_pair.first) { - const consumer_ptr ptr = m_parsers.at(key_pair.second); - const std::string metavar = get_metavar_str(ptr, key_pair.second); - size_t current_len = key_pair.second.length(); - - if (!metavar.empty()) { - current_len += metavar.length(); - } - - // For simplicity, we always include the space for the metavar - indentation = std::max(indentation, current_len + 1); - } - } - - // indentation + 4 space before description - indentation = 2 + indentation + 4; - - std::cerr << std::left << std::setw(indentation) - << "Arguments:" << "Description:\n"; + const size_t indentation = 8; cli_formatter fmt; - fmt.set_ljust(2); // Indent subsequent lines two spaces fmt.set_indent(indentation); - fmt.set_indent_first_line(false); - fmt.set_column_width(get_terminal_columns() - indentation - 3); + fmt.set_column_width(std::min(80, get_terminal_columns()) - indentation - 3); for (const auto& key_pair : keys) { if (!key_pair.first) { @@ -243,7 +223,8 @@ const std::string metavar = get_metavar_str(ptr, key_pair.second); std::cerr << std::left << std::setw(indentation) - << (" " + key_pair.second + " " + metavar); + << (" " + key_pair.second + " " + metavar) + << "\n"; std::string value = ptr->help(); if (!value.empty()) { @@ -257,6 +238,8 @@ // Format into columns and indent lines (except the first line) std::cerr << fmt.format(value) << "\n"; } + + std::cerr << "\n"; } std::cerr << std::endl; @@ -470,23 +453,12 @@ size_t knob::consume(string_vec_citer start, const string_vec_citer& end) { if (start != end) { - std::stringstream stream(*start); - int64_t temp = 0; - - if (!(stream >> temp)) { - return static_cast(-1); - } - - // Failing on trailing, non-numerical values - std::string trailing; - if (stream >> trailing) { - return static_cast(-1); - } - - if (temp >= 0 && temp <= std::numeric_limits::max()) { - *m_ptr = static_cast(temp); + try { + *m_ptr = str_to_unsigned(*start); m_value_set = true; return 1; + } catch (const std::invalid_argument&) { + return static_cast(-1); } } diff -Nru adapterremoval-2.2.2/src/argparse.hpp adapterremoval-2.2.3/src/argparse.hpp --- adapterremoval-2.2.2/src/argparse.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/argparse.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -25,9 +25,10 @@ #ifndef ARGPARSE_H #define ARGPARSE_H +#include #include +#include #include -#include #include "commontypes.hpp" diff -Nru adapterremoval-2.2.2/src/fastq_enc.cpp adapterremoval-2.2.3/src/fastq_enc.cpp --- adapterremoval-2.2.2/src/fastq_enc.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/fastq_enc.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -156,7 +156,7 @@ << "If the quality scores are Phred+33 encoded, but includes " << "scores in a greater range than expected, then use the " - << "'--maxquality' option. Note that this option effects both " + << "'--qualitymax' option. Note that this option effects both " << "reading and writing of FASTQ files.\n\n" << "See README for more information."; @@ -172,7 +172,7 @@ << "If the quality scores are Phred+64 encoded, but includes " << "scores in a greater range than expected, then use the " - << "'--maxquality' command-line option. Note that this option " + << "'--qualitymax' command-line option. Note that this option " << "effects both reading and writing of FASTQ files.\n\n" << "See README for more information."; @@ -212,7 +212,7 @@ << "If the quality scores are Solexa encoded, but includes " << "scores in a greater range than expected, then use the " - << "'--maxquality' command-line option. Note that this option " + << "'--qualitymax' command-line option. Note that this option " << "effects both reading and writing of FASTQ files.\n\n" << "See README for more information."; diff -Nru adapterremoval-2.2.2/src/fastq_enc.hpp adapterremoval-2.2.3/src/fastq_enc.hpp --- adapterremoval-2.2.2/src/fastq_enc.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/fastq_enc.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -137,7 +137,7 @@ virtual void decode(std::string& qualities) const override; /** Returns the standard name for this encoding. */ - const char* name() const; + virtual const char* name() const override; }; diff -Nru adapterremoval-2.2.2/src/fastq_io.cpp adapterremoval-2.2.3/src/fastq_io.cpp --- adapterremoval-2.2.2/src/fastq_io.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/fastq_io.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -51,14 +51,14 @@ } catch (const fastq_error& error) { print_locker lock; std::cerr << "Error reading FASTQ record at line " - << offset + dst.size() + << offset + dst.size() * 4 << "; aborting:\n" << cli_formatter::fmt(error.what()) << std::endl; throw thread_abort(); } - return dst.size(); + return dst.size() * 4; } @@ -677,7 +677,7 @@ m_eof = file_chunk->eof; if (file_chunk->buffers.empty()) { for (const auto& line : lines) { - m_output << line; + m_output.write(line.data(), line.size()); } } else { buffer_vec& buffers = file_chunk->buffers; diff -Nru adapterremoval-2.2.2/src/linereader_joined.cpp adapterremoval-2.2.3/src/linereader_joined.cpp --- adapterremoval-2.2.2/src/linereader_joined.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/linereader_joined.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -40,6 +40,7 @@ joined_line_readers::joined_line_readers(const string_vec& filenames) : m_filenames(filenames.rbegin(), filenames.rend()) , m_reader() + , m_current_line(1) { } @@ -55,6 +56,7 @@ while (dst.empty()) { if (m_reader && m_reader->getline(dst)) { + m_current_line++; break; } else if (!open_next_file()) { break; @@ -75,7 +77,9 @@ { print_locker lock; - std::cerr << "Opening FASTQ file '" << filename << "'" << std::endl; + std::cerr << "Opening FASTQ file '" << filename + << "', line numbers start at " << m_current_line + << std::endl; } m_reader.reset(new line_reader(filename)); diff -Nru adapterremoval-2.2.2/src/linereader_joined.hpp adapterremoval-2.2.3/src/linereader_joined.hpp --- adapterremoval-2.2.2/src/linereader_joined.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/linereader_joined.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -73,6 +73,8 @@ string_vec m_filenames; //! Currently open file, if any. std::unique_ptr m_reader; + //! Current line across all files. + size_t m_current_line; }; diff -Nru adapterremoval-2.2.2/src/main_adapter_rm.cpp adapterremoval-2.2.3/src/main_adapter_rm.cpp --- adapterremoval-2.2.2/src/main_adapter_rm.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/main_adapter_rm.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -48,6 +48,17 @@ typedef std::unique_ptr mt19937_ptr; +std::ostream& operator<<(std::ostream& stream, const fastq::ntrimmed& ntrim) +{ + stream << ntrim.first; + if (ntrim.first != ntrim.second) { + stream << " " << ntrim.second; + } + + return stream; +} + + void write_settings(const userconfig& config, std::ostream& output, int nth) { output << NAME << " " << VERSION @@ -123,7 +134,7 @@ } output << "\n\n[Adapter trimming]"; - if (config.max_threads > 1) { + if (config.max_threads > 1 || config.deterministic) { output << "\nRNG seed: NA"; } else { output << "\nRNG seed: " << config.seed; @@ -136,6 +147,8 @@ << "\nQuality format (output): " << config.quality_output_fmt->name() << "\nQuality score max (output): " << config.quality_output_fmt->max_score() << "\nMate-number separator (input): '" << config.mate_separator << "'" + << "\nTrimming 5p: " << config.trim_fixed_5p + << "\nTrimming 3p: " << config.trim_fixed_3p << "\nTrimming Ns: " << ((config.trim_ambiguous_bases) ? "Yes" : "No") << "\nTrimming Phred scores <= " << config.low_quality_score << ": " << (config.trim_by_quality ? "Yes" : "No") @@ -272,13 +285,69 @@ } +/** Trims fixed numbers of bases from the 5' and/or 3' termini of reads. **/ +void trim_read_termini_if_enabled(const userconfig& config, fastq& read, read_type type) +{ + size_t trim_5p = 0; + size_t trim_3p = 0; + + switch (type) { + case read_type::mate_1: + trim_5p = config.trim_fixed_5p.first; + trim_3p = config.trim_fixed_3p.first; + break; + + case read_type::mate_2: + trim_5p = config.trim_fixed_5p.second; + trim_3p = config.trim_fixed_3p.second; + break; + + case read_type::collapsed: + if (config.paired_ended_mode) { + trim_5p = config.trim_fixed_5p.first; + trim_3p = config.trim_fixed_5p.second; + } else { + trim_5p = config.trim_fixed_5p.first; + trim_3p = config.trim_fixed_3p.first; + } + break; + + default: + throw std::invalid_argument("Invalid read type in trim_read_termini_if_enabled"); + } + + if (trim_5p || trim_3p) { + read.truncate(trim_5p, read.length() - std::min(read.length(), trim_5p + trim_3p)); + } +} + + +/** Trims a read if enabled, returning the #bases removed from each end. */ +fastq::ntrimmed trim_sequence_by_quality_if_enabled(const userconfig& config, fastq& read) +{ + if (config.trim_window_length >= 0) { + return read.trim_windowed_bases(config.trim_ambiguous_bases, + config.low_quality_score, + config.trim_window_length); + } else if (config.trim_ambiguous_bases || config.trim_by_quality) { + const char quality_score = config.trim_by_quality ? config.low_quality_score : -1; + + return read.trim_trailing_bases(config.trim_ambiguous_bases, + quality_score); + } + + return fastq::ntrimmed(); +} + + void process_collapsed_read(const userconfig& config, statistics& stats, fastq& collapsed_read, fastq* mate_read, trimmed_reads& chunks) { - const fastq::ntrimmed trimmed = config.trim_sequence_by_quality_if_enabled(collapsed_read); + trim_read_termini_if_enabled(config, collapsed_read, read_type::collapsed); + const fastq::ntrimmed trimmed = trim_sequence_by_quality_if_enabled(config, collapsed_read); // If trimmed, the external coordinates are no longer reliable // for determining the size of the original template. @@ -393,7 +462,8 @@ stats->unaligned_reads++; } - m_config.trim_sequence_by_quality_if_enabled(read); + trim_read_termini_if_enabled(m_config, read, read_type::mate_1); + trim_sequence_by_quality_if_enabled(m_config, read); if (m_config.is_acceptable_read(read)) { stats->keep1++; stats->total_number_of_good_reads++; @@ -459,7 +529,11 @@ const size_t offset = m_nth * ai_analyses_offset; const char mate_separator = m_config.combined_output ? '\0' : m_config.mate_separator; - mt19937_ptr rng = m_rngs.get_sink(); + mt19937_ptr rng; + if (!m_config.deterministic) { + rng = m_rngs.get_sink(); + } + read_chunk_ptr read_chunk(dynamic_cast(chunk)); trimmed_reads chunks(m_config, offset, read_chunk->eof); statistics_ptr stats = m_stats.get_sink(); @@ -486,7 +560,7 @@ stats->number_of_reads_with_adapter.at(alignment.adapter_id) += n_adapters; if (m_config.is_alignment_collapsible(alignment)) { - fastq collapsed_read = collapse_paired_ended_sequences(alignment, read_1, read_2, *rng, + fastq collapsed_read = collapse_paired_ended_sequences(alignment, read_1, read_2, rng.get(), mate_separator); process_collapsed_read(m_config, *stats, @@ -510,9 +584,14 @@ // Undo reverse complementation (post truncation of adapters) read_2.reverse_complement(); + // Trim fixed number of bases from 5' and/or 3' termini + trim_read_termini_if_enabled(m_config, read_1, read_type::mate_1); + trim_read_termini_if_enabled(m_config, read_2, read_type::mate_2); + // Sliding window trimming or single-base trimming + trim_sequence_by_quality_if_enabled(m_config, read_1); + trim_sequence_by_quality_if_enabled(m_config, read_2); + // Are the reads good enough? Not too many Ns? - m_config.trim_sequence_by_quality_if_enabled(read_1); - m_config.trim_sequence_by_quality_if_enabled(read_2); const bool read_1_acceptable = m_config.is_acceptable_read(read_1); const bool read_2_acceptable = m_config.is_acceptable_read(read_2); diff -Nru adapterremoval-2.2.2/src/main.hpp adapterremoval-2.2.3/src/main.hpp --- adapterremoval-2.2.2/src/main.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/main.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -31,7 +31,7 @@ { const std::string NAME = "AdapterRemoval"; -const std::string VERSION = "ver. 2.2.2"; +const std::string VERSION = "ver. 2.2.3"; const std::string HELPTEXT = \ "This program searches for and removes remnant adapter sequences from\n" "your read data. The program can analyze both single end and paired end\n" diff -Nru adapterremoval-2.2.2/src/strutils.cpp adapterremoval-2.2.3/src/strutils.cpp --- adapterremoval-2.2.2/src/strutils.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/strutils.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -21,14 +21,44 @@ * You should have received a copy of the GNU General Public License * * along with this program. If not, see . * \*************************************************************************/ +#include +#include +#include + +#include #include #include + #include "strutils.hpp" namespace ar { + +unsigned str_to_unsigned(const std::string& s) +{ + std::stringstream stream(s); + int64_t temp = 0; + + if (!(stream >> temp)) { + throw std::invalid_argument("value is not a valid number"); + } + + // Failing on trailing, non-numerical values + std::string trailing; + if (stream >> trailing) { + throw std::invalid_argument("value contains trailing text"); + } + + if (temp < 0 || temp > std::numeric_limits::max()) { + throw std::invalid_argument("numerical value overflows"); + } + + return static_cast(temp); +} + + std::string toupper(const std::string& str) { std::string uppercased = str; diff -Nru adapterremoval-2.2.2/src/strutils.hpp adapterremoval-2.2.3/src/strutils.hpp --- adapterremoval-2.2.2/src/strutils.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/strutils.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -35,6 +35,16 @@ const size_t DEFAULT_INDENTATION = 4; +/** + * Convert a string to an unsigned integer. + * + * Throws std::invalid_argument if the string does not contain a proper number, + * if it contains more than just a number, or if the number overflows a + * unsigned integer. + */ +unsigned str_to_unsigned(const std::string& s); + + /** Uppercases letters in the range a-z */ std::string toupper(const std::string& str); diff -Nru adapterremoval-2.2.2/src/userconfig.cpp adapterremoval-2.2.3/src/userconfig.cpp --- adapterremoval-2.2.2/src/userconfig.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/userconfig.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -72,6 +72,30 @@ } +std::pair parse_trim_argument(const string_vec& values) +{ + unsigned mate_1 = 0; + unsigned mate_2 = 0; + + switch (values.size()) { + case 1: + mate_1 = str_to_unsigned(values.front()); + mate_2 = mate_1; + break; + + case 2: + mate_1 = str_to_unsigned(values.front()); + mate_2 = str_to_unsigned(values.back()); + break; + + default: + throw std::invalid_argument("please specify exactly one or two values"); + } + + return std::pair(mate_1, mate_2); +} + + userconfig::userconfig(const std::string& name, const std::string& version, const std::string& help) @@ -91,12 +115,15 @@ , mismatch_threshold(-1.0) , quality_input_fmt() , quality_output_fmt() + , trim_fixed_5p(0, 0) + , trim_fixed_3p(0, 0) , trim_by_quality(false) , trim_window_length(std::numeric_limits::quiet_NaN()) , low_quality_score(2) , trim_ambiguous_bases(false) , max_ambiguous_bases(1000) , collapse(false) + , deterministic(false) , shift(2) , seed(get_seed()) , max_threads(1) @@ -120,7 +147,10 @@ , interleaved(false) , identify_adapters(false) , demultiplex_sequences(false) + , trim5p() + , trim3p() { + argparser.add_header("OPTIONS:"); argparser["--file1"] = new argparse::many(&input_files_1, "FILE [FILE ...]", "Input files containing mate 1 reads or single-ended reads; " @@ -130,11 +160,19 @@ "Input files containing mate 2 reads; if used, then the same " "number of files as --file1 must be listed [OPTIONAL]."); + argparser["--identify-adapters"] = + new argparse::flag(&identify_adapters, + "Attempt to identify the adapter pair of PE reads, by searching " + "for overlapping mate reads [default: %default]."); + argparser["--threads"] = + new argparse::knob(&max_threads, "THREADS", + "Maximum number of threads [default: %default]"); + argparser.add_header("FASTQ OPTIONS:"); argparser["--qualitybase"] = new argparse::any(&quality_input_base, "BASE", "Quality base used to encode Phred scores in input; either 33, " - "64, or solexa [current: %default]."); + "64, or solexa [default: %default]."); argparser["--qualitybase-output"] = new argparse::any(&quality_output_base, "BASE", "Quality base used to encode Phred scores in output; either 33, " @@ -155,33 +193,31 @@ argparser["--interleaved"] = new argparse::flag(&interleaved, "This option enables both the --interleaved-input option and the " - "--interleaved-output option [current: %default]."); + "--interleaved-output option [default: %default]."); argparser["--interleaved-input"] = new argparse::flag(&interleaved_input, "The (single) input file provided contains both the mate 1 and " "mate 2 reads, one pair after the other, with one mate 1 reads " "followed by one mate 2 read. This option is implied by the " - "--interleaved option [current: %default]."); + "--interleaved option [default: %default]."); argparser["--interleaved-output"] = new argparse::flag(&interleaved_output, "If set, trimmed paired-end reads are written to a single file " "containing mate 1 and mate 2 reads, one pair after the other. " - "This option is implied by the --interleaved option [current: " + "This option is implied by the --interleaved option [default: " "%default]."); argparser["--combined-output"] = new argparse::flag(&combined_output, "If set, all reads are written to the same file(s), specified by " "--output1 and --output2 (--output1 only if --interleaved-output " - "is not set). Each read is further marked by either a \"PASSED\" " - "or a \"FAILED\" flag, and any read that has been FAILED " - "(including the mate for collapsed reads) are replaced with a " - "single 'N' with Phred score 0 [current: %default]."); + "is not set). Discarded reads are replaced with a single 'N' with " + "Phred score 0 [default: %default]."); argparser.add_header("OUTPUT FILES:"); argparser["--basename"] = new argparse::any(&basename, "BASENAME", "Default prefix for all output files for which no filename was " - "explicitly set [current: %default]."); + "explicitly set [default: %default]."); argparser["--settings"] = new argparse::any(nullptr, "FILE", "Output file containing information on the parameters used in the " @@ -222,17 +258,17 @@ argparser.add_header("OUTPUT COMPRESSION:"); argparser["--gzip"] = new argparse::flag(&gzip, - "Enable gzip compression [current: %default]"); + "Enable gzip compression [default: %default]"); argparser["--gzip-level"] = new argparse::knob(&gzip_level, "LEVEL", - "Compression level, 0 - 9 [current: %default]"); + "Compression level, 0 - 9 [default: %default]"); argparser["--bzip2"] = new argparse::flag(&bzip2, - "Enable bzip2 compression [current: %default]"); + "Enable bzip2 compression [default: %default]"); argparser["--bzip2-level"] = new argparse::knob(&bzip2_level, "LEVEL", - "Compression level, 0 - 9 [current: %default]"); + "Compression level, 0 - 9 [default: %default]"); argparser.add_header("TRIMMING SETTINGS:"); // Backwards compatibility with AdapterRemoval v1; not recommended due to @@ -245,43 +281,63 @@ argparser["--adapter1"] = new argparse::any(&adapter_1, "SEQUENCE", "Adapter sequence expected to be found in mate 1 reads " - "[current: %default]."); + "[default: %default]."); argparser["--adapter2"] = new argparse::any(&adapter_2, "SEQUENCE", "Adapter sequence expected to be found in mate 2 reads " - "[current: %default]."); + "[default: %default]."); argparser["--adapter-list"] = new argparse::any(&adapter_list, "FILENAME", "Read table of white-space separated adapters pairs, used as if " "the first column was supplied to --adapter1, and the second " "column was supplied to --adapter2; only the first adapter in " - "each pair is required SE trimming mode [current: %default]."); + "each pair is required SE trimming mode [default: %default]."); argparser.add_seperator(); + argparser["--minadapteroverlap"] = + new argparse::knob(&min_adapter_overlap, "LENGTH", + "In single-end mode, reads are only trimmed if the overlap " + "between read and the adapter is at least X bases long, not " + "counting ambiguous nucleotides (N); this is independent of the " + "--minalignmentlength when using --collapse, allowing a " + "conservative selection of putative complete inserts while " + "ensuring that all possible adapter contamination is trimmed " + "[default: %default]."); argparser["--mm"] = new argparse::floaty_knob(&mismatch_threshold, "MISMATCH_RATE", "Max error-rate when aligning reads and/or adapters. If > 1, the " "max error-rate is set to 1 / MISMATCH_RATE; if < 0, the defaults " "are used, otherwise the user-supplied value is used directly " - "[defaults: 1/3 for trimming; 1/10 when identifying adapters]."); - argparser["--maxns"] = - new argparse::knob(&max_ambiguous_bases, "MAX", - "Reads containing more ambiguous bases (N) than this number after " - "trimming are discarded [current: %default]."); + "[default: 1/3 for trimming; 1/10 when identifying adapters]."); argparser["--shift"] = new argparse::knob(&shift, "N", "Consider alignments where up to N nucleotides are missing from " - "the 5' termini [current: %default]."); + "the 5' termini [default: %default]."); argparser.add_seperator(); + argparser["--trim5p"] = + new argparse::many(&trim5p, "N [N]", + "Trim the 5' of reads by a fixed amount after removing adapters, " + "but before carrying out quality based trimming. Specify one " + "value to trim mate 1 and mate 2 reads the same amount, or two " + "values separated by a space to trim each mate different amounts " + "[default: no trimming]."); + argparser["--trim3p"] = + new argparse::many(&trim3p, "N [N]", + "Trim the 3' of reads by a fixed amount. See --trim5p."); + argparser["--trimns"] = new argparse::flag(&trim_ambiguous_bases, "If set, trim ambiguous bases (N) at 5'/3' termini " - "[current: %default]"); + "[default: %default]"); + argparser["--maxns"] = + new argparse::knob(&max_ambiguous_bases, "MAX", + "Reads containing more ambiguous bases (N) than this number after " + "trimming are discarded [default: %default]."); argparser["--trimqualities"] = new argparse::flag(&trim_by_quality, "If set, trim bases at 5'/3' termini with quality scores <= to " - "--minquality value [current: %default]"); + "--minquality value [default: %default]"); argparser["--trimwindows"] = new argparse::floaty_knob(&trim_window_length, "INT", "If set, quality trimming will be carried out using window based " @@ -291,20 +347,21 @@ "multiplied with the read length to determine a window size per " "read. If the resulting window size is 0 or larger than the read " "length, the read length is used as the window size. This option " - "implies --trimqualities [current: %default]."); + "implies --trimqualities [default: %default]."); argparser["--minquality"] = new argparse::knob(&low_quality_score, "PHRED", "Inclusive minimum; see --trimqualities for details " - "[current: %default]"); - + "[default: %default]"); argparser["--minlength"] = new argparse::knob(&min_genomic_length, "LENGTH", "Reads shorter than this length are discarded " - "following trimming [current: %default]."); + "following trimming [default: %default]."); argparser["--maxlength"] = new argparse::knob(&max_genomic_length, "LENGTH", "Reads longer than this length are discarded " - "following trimming [current: %default]."); + "following trimming [default: %default]."); + + argparser.add_header("READ MERGING:"); argparser["--collapse"] = new argparse::flag(&collapse, "When set, paired ended read alignments of --minalignmentlength " @@ -315,22 +372,26 @@ "reads, putative complete inserts are identified as having at " "least --minalignmentlength bases overlap with the adapter " "sequence, and are written to the the same files " - "[current: %default]."); + "[default: %default]."); + argparser["--collapse-deterministic"] = + new argparse::flag(&deterministic, + "In standard --collapse mode, AdapterRemoval will randomly select " + "one of two different overlapping bases if these have the same " + "quality (otherwise it picks the highest quality base). With " + "--collapse-deterministic, AdapterRemoval will instead set such " + "bases to N. This option implies --collapse [default: %default]."); argparser["--minalignmentlength"] = new argparse::knob(&min_alignment_length, "LENGTH", "If --collapse is set, paired reads must overlap at least this " "number of bases to be collapsed, and single-ended reads must " "overlap at least this number of bases with the adapter to be " - "considered complete template molecules [current: %default]."); - argparser["--minadapteroverlap"] = - new argparse::knob(&min_adapter_overlap, "LENGTH", - "In single-end mode, reads are only trimmed if the overlap " - "between read and the adapter is at least X bases long, not " - "counting ambiguous nucleotides (N); this is independent of the " - "--minalignmentlength when using --collapse, allowing a " - "conservative selection of putative complete inserts while " - "ensuring that all possible adapter contamination is trimmed " - "[current: %default]."); + "considered complete template molecules [default: %default]."); + argparser["--seed"] = + new argparse::knob(&seed, "SEED", + "Sets the RNG seed used when choosing between bases with equal " + "Phred scores when --collapse is enabled. This option is not " + "available if more than one thread is used. If not specified, a" + "seed is generated using the current time."); argparser.add_header("DEMULTIPLEXING:"); argparser["--barcode-list"] = @@ -339,7 +400,7 @@ "demultiplexing. Note that both indexes should be specified for " "both single-end and paired-end trimming, if double-indexed " "multiplexing was used, in order to ensure that the demultiplexed " - "reads can be trimmed correctly [current: %default]."); + "reads can be trimmed correctly [default: %default]."); argparser["--barcode-mm"] = new argparse::knob(&barcode_mm, "N", "Maximum number of mismatches allowed when counting mismatches in " @@ -357,23 +418,7 @@ argparser["--demultiplex-only"] = new argparse::flag(&demultiplex_sequences, "Only carry out demultiplexing using the list of barcodes " - "supplied with --barcode-list; do not attempt to trim adapters " - "to carry out other processing."); - - argparser.add_header("MISC:"); - argparser["--identify-adapters"] = - new argparse::flag(&identify_adapters, - "Attempt to identify the adapter pair of PE reads, by searching " - "for overlapping reads [current: %default]."); - argparser["--seed"] = - new argparse::knob(&seed, "SEED", - "Sets the RNG seed used when choosing between bases with equal " - "Phred scores when collapsing. Note that runs are not " - "deterministic if more than one thread is used. If not specified, " - "a seed is generated using the current time."); - argparser["--threads"] = - new argparse::knob(&max_threads, "THREADS", - "Maximum number of threads [current: %default]"); + "supplied with --barcode-list. No other processing is done."); } @@ -389,6 +434,9 @@ return result; } + // --collapse-deterministic implies --collapse + collapse |= deterministic; + quality_input_fmt = select_encoding("--qualitybase", quality_input_base, quality_max); if (!quality_input_fmt.get()) { return argparse::parse_result::error; @@ -546,6 +594,30 @@ << std::endl; } + try { + if (argparser.is_set("--trim5p")) { + trim_fixed_5p = parse_trim_argument(trim5p); + } + } catch (const std::invalid_argument& error) { + std::cerr << "Error: Could not parse --trim5p argument(s): " + << error.what() + << std::endl; + + return argparse::parse_result::error; + } + + try { + if (argparser.is_set("--trim3p")) { + trim_fixed_3p = parse_trim_argument(trim3p); + } + } catch (const std::invalid_argument& error) { + std::cerr << "Error: Could not parse --trim3p argument(s): " + << error.what() + << std::endl; + + return argparse::parse_result::error; + } + return argparse::parse_result::ok; } @@ -701,23 +773,6 @@ } -fastq::ntrimmed userconfig::trim_sequence_by_quality_if_enabled(fastq& read) const -{ - if (trim_window_length >= 0) { - return read.trim_windowed_bases(trim_ambiguous_bases, - low_quality_score, - trim_window_length); - } else if (trim_ambiguous_bases || trim_by_quality) { - const char quality_score = trim_by_quality ? low_quality_score : -1; - - return read.trim_trailing_bases(trim_ambiguous_bases, - quality_score); - } - - return fastq::ntrimmed(); -} - - bool check_and_set_barcode_mm(const argparse::parser& argparser, const std::string& key, unsigned barcode_mm, diff -Nru adapterremoval-2.2.2/src/userconfig.hpp adapterremoval-2.2.3/src/userconfig.hpp --- adapterremoval-2.2.2/src/userconfig.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/src/userconfig.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -27,6 +27,7 @@ #include #include +#include #include "adapterset.hpp" #include "argparse.hpp" @@ -88,9 +89,6 @@ bool is_acceptable_read(const fastq& seq) const; - /** Trims a read if enabled, returning the #bases removed from each end. */ - fastq::ntrimmed trim_sequence_by_quality_if_enabled(fastq& read) const; - //! Type of run to execute; see command ar_command run_type; @@ -132,6 +130,11 @@ //! Quality format to use when writing FASTQ records. fastq_encoding_ptr quality_output_fmt; + //! Fixed number of bases to trim from 5' for mate 1 and mate 2 reads + std::pair trim_fixed_5p; + //! Fixed number of bases to trim from 3' for mate 1 and mate 2 reads + std::pair trim_fixed_3p; + //! If true, read termini are trimmed for low-quality bases. bool trim_by_quality; //! Window size for window trimming; a fraction, whole number, or negative. @@ -148,6 +151,8 @@ //! If true, PE reads overlapping at least 'min_alignment_length' are //! collapsed to generate a higher quality consensus sequence. bool collapse; + //! Deterministic collapse; set equal-quality conflicting bases to N. + bool deterministic; // Allow for slipping basepairs by allowing missing bases in adapter unsigned shift; @@ -215,8 +220,13 @@ //! Sink for --identify-adapters bool identify_adapters; - //! Sink for --identify-adapters + //! Sink for --demultiplex-sequences bool demultiplex_sequences; + + //! Sink for --trim5p + string_vec trim5p; + //! Sink for --trim3p + string_vec trim3p; }; } // namespace ar diff -Nru adapterremoval-2.2.2/tests/alignment_test.cpp adapterremoval-2.2.3/tests/alignment_test.cpp --- adapterremoval-2.2.2/tests/alignment_test.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/alignment_test.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,1163 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#include -#include -#include -#include - -#include "testing.hpp" -#include "alignment.hpp" -#include "fastq.hpp" - -namespace ar -{ - -alignment_info new_aln(int score = 0, int offset = 0, size_t length = 0, - size_t nmm = 0, size_t nn = 0, int adapter = 0) -{ - alignment_info aln; - aln.offset = offset; - aln.score = score; - aln.length = length; - aln.n_mismatches = nmm; - aln.n_ambiguous = nn; - aln.adapter_id = adapter; - - return aln; -} - -bool operator==(const alignment_info& first, const alignment_info& second) -{ - return (first.offset == second.offset) - && (first.score == second.score) - && (first.length == second.length) - && (first.n_mismatches == second.n_mismatches) - && (first.n_ambiguous == second.n_ambiguous) - && (first.adapter_id == second.adapter_id); -} - - -std::ostream& operator<<(std::ostream& stream, const alignment_info& aln) -{ - stream << "alignment_info(" << aln.score << ", " - << aln.offset << ", " - << aln.length << ", " - << aln.n_mismatches << ", " - << aln.n_ambiguous << ", " - << aln.adapter_id << ")"; - return stream; -} - - -TEST(alignment, alignment_info) { - std::stringstream stream; - stream << new_aln(1, 2, 3, 4, 5, 6); - - ASSERT_EQ(stream.str(), "alignment_info(1, 2, 3, 4, 5, 6)"); -} - - -void ASSERT_TRUNCATED_PE_IS_UNCHANGED(const alignment_info& alignment, - const fastq& record1, - const fastq& record2) -{ - fastq tmp_record1 = record1; - fastq tmp_record2 = record2; - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, tmp_record1, tmp_record2)); - ASSERT_EQ(record1, tmp_record1); - ASSERT_EQ(record2, tmp_record2); -} - - -fastq_pair_vec create_adapter_vec(const fastq& pcr1, const fastq& pcr2 = fastq()) -{ - fastq_pair_vec adapters; - adapters.push_back(fastq_pair(pcr1, pcr2)); - return adapters; -} - - -std::random_device g_seed; -std::mt19937 g_rng(g_seed()); - - - - -/////////////////////////////////////////////////////////////////////////////// -// Cases for SE alignments (a = read 1, b = adapter, o = overlap): -// 1. No overlap = aaaaaa bbbbbb -// 2. Partial overlap = aaaaaooobbbbbb -// 3. Complete overlap = ooooooooo -// 4. a contains b = aaaaoooooo -// 5. b contains a = ooooobbbbb -// 6. a extends past b = aaaaoooooaaaa -// 7. b extends past a = bbbbooooobbbb -// 8. both extends past other = bbbbooooaaaa - - -/////////////////////////////////////////////////////////////////////////////// -// Case 1: No overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBBBBBB -// Expected result = suboptimal alignment or no overlap - -TEST(alignment_se, unalignable_sequence) -{ - const fastq record("Rec", "AAAA", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TTTT", "!!!!")); - const alignment_info expected; - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, no_expected_overlap) -{ - const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TGAGACGGT", "!!!!!!!!!")); - const alignment_info expected = new_aln(0, 6, 2, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Case 2: Partial overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBBBBBB -// Expected result = optimal alignment between ends -TEST(alignment_se, partial_overlap) -{ - const fastq record("Rec", "ACGTAGTAA", "123457890"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGTAAGGT", "!!!!!!!!")); - const alignment_info expected = new_aln(5, 4, 5); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACGT", "1234"), tmp_record); -} - - -TEST(alignment_se, partial_overlap_with_mismatch) -{ - const fastq record("Rec", "ACGTAGTAA", "123457890"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGGAAGGT", "!!!!!!!!")); - const alignment_info expected = new_aln(3, 4, 5, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACGT", "1234"), tmp_record); -} - - -TEST(alignment_se, partial_overlap_with_n) -{ - const fastq record("Rec", "ACGTAGTAA", "123457890"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGNAAGGT", "!!!!!!!!")); - const alignment_info expected = new_aln(4, 4, 5, 0, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACGT", "1234"), tmp_record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Case 3: Complete overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBB -// Expected result = Optimal alignment involving all bases - -TEST(alignment_se, completely_overlapping_sequences) -{ - const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(record); - const alignment_info expected = new_aln(8, 0, 8); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -TEST(alignment_se, completely_overlapping_sequences_with_1_mismatch) -{ - const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "GCGTAGTA", "!!!!!!!!")); - const alignment_info expected = new_aln(6, 0, 8, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -TEST(alignment_se, completely_overlapping_sequences_with_1_mismatch_and_1_n) -{ - const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq_pair_vec adapter = create_adapter_vec(fastq("Rec", "GCGTAGTN", "!!!!!!!!")); - const alignment_info expected = new_aln(5, 0, 8, 1, 1); - const alignment_info result = align_single_ended_sequence(record, adapter, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 4 and 5: Sequence A completely contains sequence B (and vice versa) -// AAAAAAAAAAA AAAA -// BBBBB BBBBBBBBBB -// Expected result = Optimal alignment involving all bases of the shortest read - -TEST(alignment_se, sequence_a_contains_b) -{ - const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGTA", "!!!!!")); - const alignment_info expected = new_aln(5, 3, 5); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACG", "ABC"), tmp_record); -} - - -TEST(alignment_se, sequence_a_contains_b__with_1_mismatch) -{ - const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TATTA", "!!!!!")); - const alignment_info expected = new_aln(3, 3, 5, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACG", "ABC"), tmp_record); -} - - -TEST(alignment_se, sequence_a_contains_b__with_1_n) -{ - const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGNA", "!!!!!")); - const alignment_info expected = new_aln(4, 3, 5, 0, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACG", "ABC"), tmp_record); -} - - -TEST(alignment_se, sequence_b_contains_a) -{ - const fastq record("Rec", "ACGT", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTA", "!!!!!!!!")); - const alignment_info expected = new_aln(4, 0, 4); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -TEST(alignment_se, sequence_b_contains_a__with_1_mismatch) -{ - const fastq record("Rec", "ACGT", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "GCGTAGTA", "!!!!!!!!")); - const alignment_info expected = new_aln(2, 0, 4, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -TEST(alignment_se, sequence_b_contains_a__with_1_n) -{ - const fastq record("Rec", "ACGT", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGNAGTA", "!!!!!!!!")); - const alignment_info expected = new_aln(3, 0, 4, 0, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 6 and 7: Sequence A extends past sequence B (and vice versa) -// AAAAAAAAAAAAAA AAAA -// BBBBB BBBBBBBBBBBBB - -TEST(alignment_se, sequence_a_extends_past_b) -{ - const fastq record("Rec", "ACGTAGTATA", "0123456789"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "AGTA", "!!!!")); - const alignment_info expected = new_aln(4, 4, 4); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "ACGT", "0123"), tmp_record); -} - - -TEST(alignment_se, sequence_b_extends_past_a__no_shift) -{ - const fastq record("Rec", "CGTA", "#!%%"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); - const alignment_info expected = new_aln(1, 3, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "CGT", "#!%"), tmp_record); -} - - -TEST(alignment_se, sequence_b_extends_past_a__shift_of_1) -{ - const fastq record("Rec", "CGTA", "#!%%"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); - const alignment_info expected = new_aln(4, -1, 4, 0, 0, 0); - const alignment_info result = align_single_ended_sequence(record, adapters, 1); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 8: Both sequences extends past the other -// AAAAAAAAAAAAAAAAAA -// BBBBBBBBBBBBBBBBBB -// Expected result = Optimal alignment involving all overlapping bases - -TEST(alignment_se, sequences_extend_past_mate) -{ - const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); - const alignment_info expected = new_aln(10, -4, 10, 0, 0, 0); - const alignment_info result = align_single_ended_sequence(record, adapters, 4); - ASSERT_EQ(expected, result); - - fastq tmp_record = record; - truncate_single_ended_sequence(result, tmp_record); - ASSERT_EQ(fastq("Rec", "", ""), tmp_record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Empty sequence or adapter - -TEST(alignment_se, empty_sequence) -{ - const fastq record; - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); - const alignment_info expected; - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, empty_adapter) -{ - const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq()); - const alignment_info expected; - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Misc - -TEST(alignment_se, shift_is_lower_than_possible) -{ - const fastq record("Rec", "AAAA", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TTTT", "!!!!")); - const alignment_info expected; - const alignment_info result = align_single_ended_sequence(record, adapters, -10); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, only_adapter_1_is_used) -{ - const fastq_pair_vec adapters = create_adapter_vec(fastq("barcode", "AAA", "JJJ"), - fastq("barcode", "TTTAAA", "JJJJJJ")); - const fastq record("Rec", "CCCCTTTAAA", "0987654321"); - const alignment_info expected = new_aln(3, 7, 3); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, prefer_best_alignement__first) -{ - fastq_pair_vec adapters; - adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); - adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); - - const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); - const alignment_info expected = new_aln(6, 9, 6); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, prefer_best_alignement__second) -{ - fastq_pair_vec adapters; - adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); - adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); - - const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); - const alignment_info expected = new_aln(6, 9, 6, 0, 0, 1); - const alignment_info result = align_single_ended_sequence(record, adapters, 0); - ASSERT_EQ(expected, result); -} - - -TEST(alignment_se, prefer_best_alignement__neither) -{ - fastq_pair_vec barcodes; - barcodes.push_back(fastq_pair(fastq("barcode", "AAAAAA", "JJJJJJ"), fastq())); - barcodes.push_back(fastq_pair(fastq("barcode", "CCCCCC", "JJJJJJ"), fastq())); - - const fastq record = fastq("Read", "AACTGTACGTAGTT", "!!!!!!10345923"); - const alignment_info result = align_single_ended_sequence(record, barcodes, 0); - ASSERT_EQ(alignment_info(), result); -} - - - -/////////////////////////////////////////////////////////////////////////////// -// Case 1 PE: No overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBBBBBB -// Expected result = suboptimal alignment or no overlap - -TEST(alignment_pe, unalignable_sequence) -{ - const fastq record1("Rec", "AAAA", "!!!!"); - const fastq record2("Rec", "TTTT", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected; - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -TEST(alignment_pe, no_expected_overlap) -{ - const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq record2("Rec", "TGAGACGGT", "!!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(0, 6, 2, 1); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Case 2 PE: Partial overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBBBBBB -// Expected result = optimal alignment between ends - -TEST(alignment_pe, partial_overlap) -{ - const fastq record1("Rec", "ACGTAGTAA", "!!!!!!!!!"); - const fastq record2("Rec", "AGTAAGGT", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(5, 4, 5); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Case 3 PE: Complete overlap between sequences: -// AAAAAAAAAAA -// BBBBBBBBBBB -// Expected result = Optimal alignment involving all bases - -TEST(alignment_pe, completely_overlapping_sequences) -{ - const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); - const fastq record2 = record1; - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(8, 0, 8); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 4 and 5 PE: Sequence A completely contains sequence B (and vice versa) -// AAAAAAAAAAA AAAA -// BBBBB BBBBBBBBBB -// Expected result = Optimal alignment involving all bases of the shortest read - -TEST(alignment_pe, sequence_a_contains_b) -{ - const fastq record1("Rec1", "ACGTAGTA", "!!!!!!!!"); - const fastq record2("Rec2", "TAGTA", "!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(5, 3, 5); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -TEST(alignment_pe, sequence_b_contains_a) -{ - const fastq record1("Rec1", "ACGT", "!!!!"); - const fastq record2("Rec2", "ACGTAGTA", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(4, 0, 4); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 6 and 7 PE: Sequence A extends past sequence B (and vice versa) -// AAAAAAAAAAAAAA AAAA -// BBBBB BBBBBBBBBBBBB - -TEST(alignment_pe, sequence_a_extends_past_b) -{ - const fastq record1("Rec1", "ACGTAGTACG", "!!!!!!!!!!"); - const fastq record2("Rec2", "AGTA", "!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(6, 4, 6); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record1 = record1; - fastq tmp_record2 = record2; - ASSERT_EQ(1, truncate_paired_ended_sequences(result, tmp_record1, tmp_record2)); - ASSERT_EQ(fastq("Rec1", "ACGTAGTA", "!!!!!!!!"), tmp_record1); - ASSERT_EQ(fastq("Rec2", "AGTA", "!!!!"), tmp_record2); -} - - -TEST(alignment_pe, sequence_b_extends_past_a) -{ - const fastq record1("Rec1", "CGTA", "!!!!"); - const fastq record2("Rec2", "ACCGTAGTAT", "!!!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(6, -2, 6); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record1 = record1; - fastq tmp_record2 = record2; - ASSERT_EQ(1, truncate_paired_ended_sequences(result, tmp_record1, tmp_record2)); - ASSERT_EQ(fastq("Rec1", "CGTA", "!!!!"), tmp_record1); - ASSERT_EQ(fastq("Rec2", "CGTAGTAT", "!!!!!!!!"), tmp_record2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Cases 8 PE: Both sequences extends past the other -// AAAAAAAAAAAAAAAAAA -// BBBBBBBBBBBBBBBBBB -// Expected result = Optimal alignment involving all overlapping bases - -TEST(alignment_pe, sequences_extend_past_mate) -{ - const fastq record1("Rec1", "ACGTAGTATACGCT", "!!!!!!!!!!!!!!"); - const fastq record2("Rec2", "GTACACGTAGTATA", "!!!!!!!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(18, -4, 18); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - - fastq tmp_record1 = record1; - fastq tmp_record2 = record2; - ASSERT_EQ(2, truncate_paired_ended_sequences(result, tmp_record1, tmp_record2)); - ASSERT_EQ(fastq("Rec1", "ACGTAGTATA", "!!!!!!!!!!"), tmp_record1); - ASSERT_EQ(fastq("Rec2", "ACGTAGTATA", "!!!!!!!!!!"), tmp_record2); -} - - -TEST(alignment_pe, only_adadapter_sequence) -{ - const fastq record1("Rec1", "CCCGAC", "!!!!!!"); - const fastq record2("Rec2", "ATGCCTT", "!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), - fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); - - ASSERT_EQ(new_aln(13, -7, 13), align_paired_ended_sequences(record1, record2, adapters, 0)); -} - - -TEST(alignment_pe, only_adadapter_sequence__missing_base__shift) -{ - // Test the case where both reads are adapters, but are missing a single base - // Normally, alignments that do not invovle read1 vs read2 are skipped, but - // missing bases may cause some alignments to be missed. - const fastq record1("Rec1", "CCGACC", "!!!!!!"); - const fastq record2("Rec2", "ATGCCT", "!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), - fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); - - // Sub-optimal alignment: - // aagatgccttCCGACC - // ATGCCTcccgacccgt - ASSERT_EQ(new_aln( 1, -3, 9, 4), align_paired_ended_sequences(record1, record2, adapters, 0)); - // Optimal alignment, only possible with shift - // aagatgccttCCGACC - // ATGCCTcccgacccgt - ASSERT_EQ(new_aln(11, -7, 13, 1), align_paired_ended_sequences(record1, record2, adapters, 1)); -} - - -TEST(alignment_pe, invalid_alignment) -{ - fastq record1("Rec", "", ""); - fastq record2("Rec", "", ""); - const alignment_info alignment = new_aln(0, 1); - - ASSERT_THROW(truncate_paired_ended_sequences(alignment, record1, record2), std::invalid_argument); -} - - -/////////////////////////////////////////////////////////////////////////////// - -TEST(alignment_pe, empty_mate_1) -{ - const fastq record1("Rec", "ACGTAGTAA", "!!!!!!!!!"); - const fastq record2("Rec", "AGTAAGGT", "!!!!!!!!"); - const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), - fastq("PCR2", "TGTAC", "!!!!!")); - const alignment_info expected = new_aln(5, 4, 5); - const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); - ASSERT_EQ(expected, result); - ASSERT_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); - -} - - -/////////////////////////////////////////////////////////////////////////////// -// Collapsing of reads - -TEST(collapsing, partial_overlap) -{ - fastq record1("Rec1", "ATATTATA", "01234567"); - fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 4); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATATTATAACGT", "01234567EFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, complete_overlap_both_directions) -{ - fastq record1("Rec1", "ATATTATAA", "JJJJJJJJJ"); - fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); - const alignment_info alignment = new_aln(0, -1); - ASSERT_EQ(2, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, complete_overlap_mate_1) -{ - fastq record1("Rec1", "ATATTATAG", "JJJJJJJJJ"); - fastq record2("Rec2", "ATATTATA", "JJJJJJJJ"); - const alignment_info alignment = new_aln(); - ASSERT_EQ(1, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, complete_overlap_mate_2) -{ - fastq record1("Rec1", "ATATTATA", "JJJJJJJJ"); - fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); - const alignment_info alignment = new_aln(0, -1); - ASSERT_EQ(1, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, unequal_sequence_length__mate_1_shorter) -{ - fastq record1("Rec1", "ATA", "012"); - fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 3); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATANNNNACGT", "012ABCDEFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, unequal_sequence_length__mate_1_shorter__mate_2_extends_past) -{ - fastq record1("Rec1", "ATA", "012"); - fastq record2("Rec2", "AANNNNACGT", "90ABCDEFGH"); - const alignment_info alignment = new_aln(0, -2); - ASSERT_EQ(1, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATANACGT", "012DEFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, unequal_sequence_length__mate_2_shorter) -{ - fastq record1("Rec1", "ATATTATA", "01234567"); - fastq record2("Rec2", "ACG", "EFG"); - const alignment_info alignment = new_aln(0, 8); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ATATTATAACG", "01234567EFG"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, ambiguous_sites_are_filled_from_the_mate) -{ - fastq record1("Rec1", "NNNNNNTATA", "0123456789"); - fastq record2("Rec2", "ACGTNNNNNN", "ABCDEFGHIJ"); - const alignment_info alignment; - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "ACGTNNTATA", "ABCD!!6789"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, consensus_bases__identical_nucleotides) -{ - fastq record1("Rec1", "GCATGATATA", "012345!0:A"); - fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); - const alignment_info alignment = new_aln(0, 6); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345(FBcEFGHIJ", FASTQ_ENCODING_SAM); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, consensus_bases__identical_nucleotides__scores_are_capped_at_41) -{ - fastq record1("Rec1", "GCATGATATA", "0123456789"); - fastq record2("Rec2", "TATATACAAC", "ABCDEFGHIJ"); - const alignment_info alignment = new_aln(0, 6); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345Z\\^`EFGHIJ", FASTQ_ENCODING_SAM); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, consensus_bases__different_nucleotides) -{ - fastq record1("Rec1", "GCATGAGCAT", "012345!0:A"); - fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); - const alignment_info alignment = new_aln(0, 6); - ASSERT_EQ(0, truncate_paired_ended_sequences(alignment, record1, record2)); - const fastq collapsed_expected = fastq("Rec1", "GCATGATAATTACAAC", "012345(%5%EFGHIJ"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, consensus_bases__different_nucleotides__same_quality_1) -{ - const fastq record1("Rec1", "G", "1"); - const fastq record2("Rec2", "T", "1"); - const alignment_info alignment; - std::seed_seq seed{1}; - std::mt19937 rng(seed); - - const fastq collapsed_expected = fastq("Rec1", "G", "#"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, consensus_bases__different_nucleotides__same_quality_2) -{ - const fastq record1("Rec1", "G", "1"); - const fastq record2("Rec2", "T", "1"); - const alignment_info alignment; - std::seed_seq seed{2}; - std::mt19937 rng(seed); - - const fastq collapsed_expected = fastq("Rec1", "T", "#"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, rng); - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, offset_past_the_end) -{ - const fastq record1("Rec1", "G", "1"); - const fastq record2("Rec2", "T", "1"); - const alignment_info alignment = new_aln(0, 2); - ASSERT_THROW(collapse_paired_ended_sequences(alignment, record1, record2, g_rng), std::invalid_argument); -} - - -TEST(collapsing, partial_overlap__mate_numbers_removed) -{ - const fastq record1("Read/1", "ATATTATA", "01234567"); - const fastq record2("Read/2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 4); - const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, partial_overlap__mate_numbers_removed__mate_1_meta_kept) -{ - const fastq record1("Read/1 Meta1", "ATATTATA", "01234567"); - const fastq record2("Read/2 Meta2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 4); - const fastq collapsed_expected = fastq("Read Meta1", "ATATTATAACGT", "01234567EFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, partial_overlap__mate_numbers_removed__non_std_mate_sep) -{ - const fastq record1("Read:1", "ATATTATA", "01234567"); - const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 4); - const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng, ':'); - - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -TEST(collapsing, partial_overlap__mate_numbers_removed__non_std_mate_sep__not_set) -{ - const fastq record1("Read:1", "ATATTATA", "01234567"); - const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); - const alignment_info alignment = new_aln(0, 4); - const fastq collapsed_expected = fastq("Read:1", "ATATTATAACGT", "01234567EFGH"); - const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); - - ASSERT_EQ(collapsed_expected, collapsed_result); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Barcode extraction - -TEST(extract_adapter_sequences, empty_sequences) -{ - const fastq expected_1 = fastq("read1", "", ""); - const fastq expected_2 = fastq("read2", "", ""); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(alignment_info(), read1, read2); - ASSERT_EQ(expected_1, read1); - ASSERT_EQ(expected_2, read2); -} - - -TEST(extract_adapter_sequences, empty_sequence_1) -{ - const fastq expected_1 = fastq("read1", "", ""); - const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = fastq("read2", "GGGGCC", "!!!!!!"); - extract_adapter_sequences(alignment_info(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, empty_sequence_2) -{ - const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "", ""); - fastq read1 = fastq("read1", "", ""); - fastq read2 = expected_2; - extract_adapter_sequences(alignment_info(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, empty_sequence_3) -{ - const fastq expected_1 = fastq("read1", "", ""); - const fastq expected_2 = fastq("read2", "", ""); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(alignment_info(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_1_no_alignment) -{ - const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(alignment_info(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_2_partial_overlap) -{ - const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(0, 2), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); - -} - - -TEST(extract_adapter_sequences, case_3_complete_overlap) -{ - const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_4_read1_contains_read2) -{ - const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "GGCC", "!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(0, 2), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_5_read2_contains_read1) -{ - const fastq expected_1 = fastq("read1", "AATT", "!!!!"); - const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_6_read1_extends_past_read2) -{ - const fastq expected_1 = fastq("read1", "AATTTTCC", "12345678"); - const fastq expected_2 = fastq("read2", "GGGGGG", "!!!!!!"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(), read1, read2); - ASSERT_EQ(fastq("read1", "CC", "78"), read1); - ASSERT_EQ(fastq("read2", "", ""), read2); -} - - -TEST(extract_adapter_sequences, case_7_read2_extends_past_read1) -{ - const fastq expected_1 = fastq("read1", "TTTTTT", "!!!!!!"); - const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(0, -2), read1, read2); - ASSERT_EQ(fastq("read1", "", ""), read1); - ASSERT_EQ(fastq("read2", "AA", "12"), read2); -} - - -TEST(extract_adapter_sequences, case_8_reads_extends_past_each_pther) -{ - const fastq expected_1 = fastq("read1", "TTTTTTCCC", "ABCDEFGHI"); - const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); - fastq read1 = expected_1; - fastq read2 = expected_2; - extract_adapter_sequences(new_aln(0, -2), read1, read2); - ASSERT_EQ(fastq("read1", "CCC", "GHI"), read1); - ASSERT_EQ(fastq("read2", "AA", "12"), read2); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Brute-force checking of alignment calculations -// Simply check all combinations involving 3 bases varying, for a range of -// sequence lengths to help catch corner cases with the optimizations - -// The function is not exposed, so a declaration is required -bool compare_subsequences(const alignment_info& best, alignment_info& current, - const char* seq_1_ptr, const char* seq_2_ptr); - - -/** Naive reimplementation of alignment calculation. **/ -void update_alignment(alignment_info& aln, - const std::string& a, - const std::string& b, - size_t nbases) -{ - ASSERT_EQ(a.length(), b.length()); - - for (size_t i = 0; i < nbases; ++i) { - const char nt1 = a.at(i); - const char nt2 = b.at(i); - - if (nt1 == 'N' || nt2 == 'N') { - aln.n_ambiguous++; - } else if (nt1 == nt2) { - aln.score++; - } else { - aln.n_mismatches++; - aln.score--; - } - } -} - - -/** Returns all 3 nt combinations of the bases ACGTN. **/ -std::vector get_combinations() -{ - std::vector result; - const std::string nts = "ACGTN"; - for (size_t i = 0; i < nts.length(); ++i) { - for (size_t j = 0; j < nts.length(); ++j) { - for (size_t k = 0; k < nts.length(); ++k) { - std::string combination(3, 'A'); - combination.at(0) = nts.at(i); - combination.at(1) = nts.at(j); - combination.at(2) = nts.at(k); - result.push_back(combination); - } - } - } - - return result; -} - - -TEST(compare_subsequences, brute_force_validation) -{ - const alignment_info best; - const std::vector combinations = get_combinations(); - for (size_t seqlen = 10; seqlen <= 20; ++seqlen) { - for (size_t pos = 0; pos < seqlen; ++pos) { - const size_t nbases = std::min(3, seqlen - pos); - - for (size_t i = 0; i < combinations.size(); ++i) { - for (size_t j = 0; j < combinations.size(); ++j) { - alignment_info expected; - expected.length = seqlen; - expected.score = seqlen - nbases; - update_alignment(expected, combinations.at(i), combinations.at(j), nbases); - - std::string mate1 = std::string(seqlen, 'A'); - mate1.replace(pos, nbases, combinations.at(i).substr(0, nbases)); - std::string mate2 = std::string(seqlen, 'A'); - mate2.replace(pos, nbases, combinations.at(j).substr(0, nbases)); - - alignment_info current; - current.length = seqlen; - compare_subsequences(best, current, mate1.c_str(), mate2.c_str()); - - ASSERT_EQ(expected, current); - } - } - } - } -} - -} // namespace ar diff -Nru adapterremoval-2.2.2/tests/argparse_test.cpp adapterremoval-2.2.3/tests/argparse_test.cpp --- adapterremoval-2.2.2/tests/argparse_test.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/argparse_test.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,511 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#include -#include -#include -#include - -#include "argparse.hpp" -#include "debug.hpp" - -namespace ar -{ - -typedef std::unique_ptr consumer_autoptr; - - -/////////////////////////////////////////////////////////////////////////////// -// flag -- boolean - -TEST(flag, defaults) -{ - consumer_autoptr ptr(new argparse::flag()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(" ", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("off", ptr->to_str()); -} - - -TEST(flag, help) -{ - consumer_autoptr ptr(new argparse::flag(NULL, "help! help!")); - ASSERT_EQ("help! help!", ptr->help()); -} - - -TEST(flag, consumes_zero_arguments) -{ - string_vec arguments; - arguments.push_back("--foo"); - consumer_autoptr ptr(new argparse::flag()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(0, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); -} - - -TEST(flag, consume_past_the_end) -{ - const string_vec arguments; - consumer_autoptr ptr(new argparse::flag()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(0, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); -} - - -TEST(flag, consume__with_sink__true) -{ - bool sink = true; - consumer_autoptr ptr(new argparse::flag(&sink)); - ASSERT_EQ("on", ptr->to_str()); - const string_vec arguments; - ASSERT_EQ(0, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_TRUE(sink); - ASSERT_EQ("on", ptr->to_str()); -} - - -TEST(flag, consume__with_sink__false) -{ - bool sink = false; - consumer_autoptr ptr(new argparse::flag(&sink)); - ASSERT_EQ("off", ptr->to_str()); - const string_vec arguments; - ASSERT_EQ(0, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_TRUE(sink); - ASSERT_EQ("on", ptr->to_str()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// any -- string - -TEST(any, defaults) -{ - consumer_autoptr ptr(new argparse::any()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("", ptr->to_str()); -} - - -TEST(any, args_set) -{ - std::string sink = "kitchensink"; - consumer_autoptr ptr(new argparse::any(&sink, "a metavar", "help!")); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("a metavar", ptr->metavar()); - ASSERT_EQ("help!", ptr->help()); - ASSERT_EQ("kitchensink", ptr->to_str()); -} - - -TEST(any, consumes_one_argument) -{ - string_vec arguments; - arguments.push_back("foo"); - arguments.push_back("bar"); - consumer_autoptr ptr(new argparse::any()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo", ptr->to_str()); -} - - -TEST(any, consume_past_the_end) -{ - const string_vec arguments; - consumer_autoptr ptr(new argparse::any()); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(static_cast(-1), ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->to_str()); -} - - -TEST(any, consume__with_sink__empty) -{ - std::string sink; - consumer_autoptr ptr(new argparse::any(&sink)); - ASSERT_EQ("", ptr->to_str()); - string_vec arguments; - arguments.push_back("foo"); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo", sink); - ASSERT_EQ("foo", ptr->to_str()); -} - - -TEST(any, consume__with_sink__preset) -{ - std::string sink = "kitchensink"; - consumer_autoptr ptr(new argparse::any(&sink)); - ASSERT_EQ("kitchensink", ptr->to_str()); - string_vec arguments; - arguments.push_back("foo"); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo", sink); - ASSERT_EQ("foo", ptr->to_str()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// many -- strings - -TEST(many, defaults) -{ - string_vec sink; - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("", ptr->to_str()); -} - - -TEST(many, args_set) -{ - string_vec sink; - sink.push_back("kitchensink"); - - consumer_autoptr ptr(new argparse::many(&sink, "a metavar", "help!")); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("a metavar", ptr->metavar()); - ASSERT_EQ("help!", ptr->help()); - ASSERT_EQ("kitchensink", ptr->to_str()); -} - - -TEST(many, consumes_one_argument) -{ - string_vec arguments; - arguments.push_back("foo"); - - string_vec sink; - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo", ptr->to_str()); -} - - -TEST(many, consumes_two_arguments) -{ - string_vec arguments; - arguments.push_back("foo"); - arguments.push_back("bar"); - - string_vec sink; - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(2, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo;bar", ptr->to_str()); -} - - -TEST(many, consumes_until_next) -{ - string_vec arguments; - arguments.push_back("foo"); - arguments.push_back("--zoo"); - arguments.push_back("bar"); - - string_vec sink; - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("foo", ptr->to_str()); -} - - -TEST(many, consume_past_the_end) -{ - string_vec sink; - const string_vec arguments; - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(0, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ("", ptr->to_str()); -} - - -TEST(many, consume__with_sink__empty) -{ - string_vec sink; - string_vec expected; - expected.push_back("foo"); - - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_EQ("", ptr->to_str()); - string_vec arguments; - arguments.push_back("foo"); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(expected, sink); - ASSERT_EQ("foo", ptr->to_str()); -} - - -TEST(many, consume__with_sink__preset) -{ - string_vec sink; - sink.push_back("kitchensink"); - string_vec expected; - expected.push_back("foo"); - - consumer_autoptr ptr(new argparse::many(&sink)); - ASSERT_EQ("kitchensink", ptr->to_str()); - string_vec arguments; - arguments.push_back("foo"); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(expected, sink); - ASSERT_EQ("foo", ptr->to_str()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// knob -- unsigned - -TEST(knob, defaults) -{ - unsigned sink = 0; - consumer_autoptr ptr(new argparse::knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("0", ptr->to_str()); -} - - -TEST(knob, defaults__sink_required) -{ - ASSERT_THROW(argparse::knob(NULL), assert_failed); -} - - -TEST(knob, args_set) -{ - unsigned sink = 7913; - consumer_autoptr ptr(new argparse::knob(&sink, "a metavar", "help!")); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("a metavar", ptr->metavar()); - ASSERT_EQ("help!", ptr->help()); - ASSERT_EQ("7913", ptr->to_str()); -} - - -TEST(knob, consumes_one_argument) -{ - unsigned sink = 0; - string_vec arguments; - arguments.push_back("47"); - arguments.push_back("bar"); - consumer_autoptr ptr(new argparse::knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(47, sink); - ASSERT_EQ("47", ptr->to_str()); -} - - -TEST(knob, consume_past_the_end) -{ - unsigned sink = 13; - const string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(static_cast(-1), ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(13, sink); - ASSERT_EQ("13", ptr->to_str()); -} - - -TEST(knob, reject_negative_values) -{ - unsigned sink = 13; - string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - arguments.push_back("-47"); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(static_cast(-1), ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(13, sink); - ASSERT_EQ("13", ptr->to_str()); -} - - -TEST(knob, accept_zero) -{ - unsigned sink = 13; - string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - arguments.push_back("0"); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(0, sink); - ASSERT_EQ("0", ptr->to_str()); -} - - -TEST(knob, upper_bound) -{ - unsigned sink = 13; - string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - arguments.push_back("4294967295"); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(4294967295, sink); - ASSERT_EQ("4294967295", ptr->to_str()); -} - - -TEST(knob, past_upper_bound) -{ - unsigned sink = 13; - string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - arguments.push_back("4294967296"); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(-1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); -} - - -TEST(knob, trailing_garbage) -{ - unsigned sink = 13; - string_vec arguments; - consumer_autoptr ptr(new argparse::knob(&sink)); - arguments.push_back("7913w"); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(-1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// floaty_knob -- double - -TEST(floaty_knob, defaults) -{ - double sink = 0; - consumer_autoptr ptr(new argparse::floaty_knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("0", ptr->to_str()); -} - - -TEST(floaty_knob, default_nan) -{ - double sink = std::numeric_limits::quiet_NaN(); - consumer_autoptr ptr(new argparse::floaty_knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("", ptr->metavar()); - ASSERT_EQ("", ptr->help()); - ASSERT_EQ("", ptr->to_str()); -} - - -TEST(floaty_knob, defaults__sink_required) -{ - ASSERT_THROW(argparse::floaty_knob(NULL), assert_failed); -} - - -TEST(floaty_knob, args_set) -{ - double sink = 3.142; - consumer_autoptr ptr(new argparse::floaty_knob(&sink, "a metavar", "help!")); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ("a metavar", ptr->metavar()); - ASSERT_EQ("help!", ptr->help()); - ASSERT_EQ("3.142", ptr->to_str()); -} - - -TEST(floaty_knob, consumes_one_argument) -{ - double sink = 47.0; - string_vec arguments; - arguments.push_back("-19.84"); - arguments.push_back("bar"); - consumer_autoptr ptr(new argparse::floaty_knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_TRUE(ptr->is_set()); - ASSERT_EQ(-19.84, sink); - ASSERT_EQ("-19.84", ptr->to_str()); -} - - -TEST(floaty_knob, consume_past_the_end) -{ - double sink = 13; - const string_vec arguments; - consumer_autoptr ptr(new argparse::floaty_knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(static_cast(-1), ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(13, sink); - ASSERT_EQ("13", ptr->to_str()); -} - - -TEST(floaty_knob, trailing_garbage) -{ - double sink = 47.0; - string_vec arguments; - arguments.push_back("-19.84wat"); - consumer_autoptr ptr(new argparse::floaty_knob(&sink)); - ASSERT_FALSE(ptr->is_set()); - ASSERT_EQ(-1, ptr->consume(arguments.begin(), arguments.end())); - ASSERT_FALSE(ptr->is_set()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// parser - -} // namespace ar diff -Nru adapterremoval-2.2.2/tests/fastq_enc_test.cpp adapterremoval-2.2.3/tests/fastq_enc_test.cpp --- adapterremoval-2.2.2/tests/fastq_enc_test.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/fastq_enc_test.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,48 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#include -#include -#include - -#include "testing.hpp" -#include "debug.hpp" -#include "fastq.hpp" - - -namespace ar -{ - -/////////////////////////////////////////////////////////////////////////////// -// Names (default objects) - -TEST(fastq_enc, global_objects__name) -{ - ASSERT_STREQ("Phred+33", FASTQ_ENCODING_33.name()); - ASSERT_STREQ("Phred+64", FASTQ_ENCODING_64.name()); - ASSERT_STREQ("Phred+33", FASTQ_ENCODING_SAM.name()); - ASSERT_STREQ("Solexa", FASTQ_ENCODING_SOLEXA.name()); -} - -} diff -Nru adapterremoval-2.2.2/tests/fastq_test.cpp adapterremoval-2.2.3/tests/fastq_test.cpp --- adapterremoval-2.2.2/tests/fastq_test.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/fastq_test.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,1142 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#include -#include -#include - -#include "testing.hpp" -#include "debug.hpp" -#include "fastq.hpp" -#include "linereader.hpp" - -namespace ar -{ - -class vec_reader : public line_reader_base -{ -public: - vec_reader(const string_vec& lines) - : m_lines(lines) - , m_it(m_lines.begin()) - { - } - - bool getline(std::string& dst) { - if (m_it == m_lines.end()) { - return false; - } - - dst = *m_it++; - return true; - } - -private: - string_vec m_lines; - string_vec::const_iterator m_it; -}; - - - -/////////////////////////////////////////////////////////////////////////////// -// Default constructor - -TEST(fastq, default_constructor) -{ - const fastq record; - ASSERT_EQ("", record.header()); - ASSERT_EQ("", record.sequence()); - ASSERT_EQ("", record.qualities()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Primary constructor - -TEST(fastq, constructor_empty_fields) -{ - const fastq record("", "", ""); - ASSERT_EQ("", record.header()); - ASSERT_EQ("", record.sequence()); - ASSERT_EQ("", record.qualities()); -} - - -TEST(fastq, constructor_simple_record_phred_33_encoded) -{ - const fastq record("record_1", "ACGAGTCA", "!7BF8DGI"); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); -} - - -TEST(fastq, constructor_simple_record_phred_64_encoded) -{ - const fastq record("record_2", "ACGAGTCA", "@VaeWcfh", FASTQ_ENCODING_64); - ASSERT_EQ("record_2", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); -} - - -TEST(fastq, constructor_simple_record_phred_solexa_encoded) -{ - const fastq record("record_3", "AAACGAGTCA", ";h>S\\TCDUJ", FASTQ_ENCODING_SOLEXA); - ASSERT_EQ("record_3", record.header()); - ASSERT_EQ("AAACGAGTCA", record.sequence()); - ASSERT_EQ("\"I#4=5&&6+", record.qualities()); -} - - -TEST(fastq, constructor_simple_record_lowercase_to_uppercase) -{ - const fastq record("record_1", "AnGaGtcA", "!7BF8DGI"); - ASSERT_EQ("ANGAGTCA", record.sequence()); -} - - -TEST(fastq, constructor_simple_record_dots_to_n) -{ - const fastq record("record_1", "AC.AG.C.", "!7BF8DGI"); - ASSERT_EQ("ACNAGNCN", record.sequence()); -} - - -TEST(fastq, constructor_score_boundries_phred_33) -{ - ASSERT_NO_THROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_33)); - ASSERT_THROW(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_33), fastq_error); - - ASSERT_NO_THROW(fastq("Rec", "CAT", "IJJ", FASTQ_ENCODING_33)); - ASSERT_THROW(fastq("Rec", "CAT", "IJK", FASTQ_ENCODING_33), fastq_error); -} - - -TEST(fastq, constructor_score_boundries_phred_64) -{ - ASSERT_NO_THROW(fastq("Rec", "CAT", "@@A", FASTQ_ENCODING_64)); - ASSERT_THROW(fastq("Rec", "CAT", "?@A", FASTQ_ENCODING_64), fastq_error); - - ASSERT_NO_THROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_64)); - ASSERT_THROW(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_64), fastq_error); -} - - -TEST(fastq, constructor_score_boundries_solexa) -{ - ASSERT_NO_THROW(fastq("Rec", "CAT", ";;<", FASTQ_ENCODING_SOLEXA)); - ASSERT_THROW(fastq("Rec", "CAT", ":;<", FASTQ_ENCODING_SOLEXA), fastq_error); - - ASSERT_NO_THROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_SOLEXA)); - ASSERT_THROW(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_SOLEXA), fastq_error); -} - -TEST(fastq, constructor_score_boundries_ignored) -{ - ASSERT_NO_THROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_SAM)); - ASSERT_THROW(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_SAM), fastq_error); - - ASSERT_NO_THROW(fastq("Rec", "CAT", "gh~", FASTQ_ENCODING_SAM)); - ASSERT_THROW(fastq("Rec", "CAT", "gh\x7f", FASTQ_ENCODING_SAM), fastq_error); -} - - -TEST(fastq, constructor_field_lengths) -{ - ASSERT_NO_THROW(fastq("Name", "CAT", "IJJ")); - // A non-empty sequence must be specified - ASSERT_THROW(fastq("Name", "", "IJJ"), fastq_error); - // A non-empty quality string must be specified - ASSERT_THROW(fastq("Name", "CAT", ""), fastq_error); - // And the length of each must be the same - ASSERT_THROW(fastq("Name", "CA", "IJJ"), fastq_error); - ASSERT_THROW(fastq("Name", "CAT", "IJ"), fastq_error); -} - - -TEST(fastq, constructor_invalid_nucleotides) -{ - ASSERT_NO_THROW(fastq("Name", "CATT", "IJJI")); - // Non-alpha characters are not allowed - ASSERT_THROW(fastq("Name", "CAT!", "IJJI"), fastq_error); - // Numeric charecters are not allowed - ASSERT_THROW(fastq("Name", "CAT7", "IJJI"), fastq_error); - // But neither are non acgtn/ACGTN allowed - ASSERT_THROW(fastq("Name", "CATS", "IJJI"), fastq_error); - ASSERT_THROW(fastq("Name", "CATs", "IJJI"), fastq_error); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Constructor without qualities - -TEST(fastq, constructor_no_qualities) -{ - const fastq record("record_1", "ACGT"); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("ACGT", record.sequence()); - ASSERT_EQ("!!!!", record.qualities()); -} - - -TEST(fastq, constructor_no_qualities_no_sequence) -{ - const fastq record("record_1", ""); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("", record.sequence()); - ASSERT_EQ("", record.qualities()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// misc properties - -TEST(fastq, name) -{ - ASSERT_EQ("name", fastq("name", "", "").name()); - ASSERT_EQ("name", fastq("name meta", "", "").name()); - ASSERT_EQ("name", fastq("name meta more", "", "").name()); -} - - -TEST(fastq, length) -{ - ASSERT_EQ(0, fastq("record_1", "", "").length()); - ASSERT_EQ(1, fastq("record_1", "A", "G").length()); - ASSERT_EQ(2, fastq("record_1", "AC", "!B").length()); - ASSERT_EQ(3, fastq("record_1", "ACG", "!7B").length()); -} - - -TEST(fastq, count_ns) -{ - ASSERT_EQ(0, fastq("Rec", "ACGTA", "IJIJI").count_ns()); - ASSERT_EQ(1, fastq("Rec", "ANGTA", "IJIJI").count_ns()); - ASSERT_EQ(2, fastq("Rec", "ANGTN", "IJIJI").count_ns()); - ASSERT_EQ(3, fastq("Rec", "ANGNN", "IJIJI").count_ns()); - ASSERT_EQ(4, fastq("Rec", "NNGNN", "IJIJI").count_ns()); - ASSERT_EQ(5, fastq("Rec", "NNNNN", "IJIJI").count_ns()); -} - - -/////////////////////////////////////////////////////////////////////////////// -// trim_trailing_bases - -TEST(fastq, trim_trailing_bases__empty_record) -{ - fastq record("Empty", "", ""); - const fastq::ntrimmed expected(0, 0); - ASSERT_EQ(expected, record.trim_trailing_bases(true, 10)); - ASSERT_EQ(fastq("Empty", "", ""), record); -} - - -TEST(fastq, trim_trailing_bases__trim_nothing) -{ - const fastq reference("Rec", "NNNNN", "!!!!!"); - const fastq::ntrimmed expected(0, 0); - fastq record = reference; - - // Trim neither Ns nor low Phred score bases - ASSERT_EQ(expected, record.trim_trailing_bases(false, -1)); - ASSERT_EQ(reference, record); -} - - -TEST(fastq, trim_trailing_bases__trim_ns) -{ - fastq record("Rec", "NNANT", "23456"); - const fastq expected_record("Rec", "ANT", "456"); - const fastq::ntrimmed expected_ntrim(2, 0); - - ASSERT_EQ(expected_ntrim, record.trim_trailing_bases(true, -1)); - ASSERT_EQ(expected_record, record); -} - - -TEST(fastq, trim_trailing_bases__trim_trailing_bases) -{ - const fastq expected_record("Rec", "TN", "%$"); - const fastq::ntrimmed expected_ntrim(0, 3); - fastq record("Rec", "TNANT", "%$#!\""); - - ASSERT_EQ(expected_ntrim, record.trim_trailing_bases(false, 2)); - ASSERT_EQ(expected_record, record); -} - - -TEST(fastq, trim_trailing_bases__trim_mixed) -{ - const fastq expected_record("Rec", "TAG", "$12"); - const fastq::ntrimmed expected_ntrim(3, 2); - fastq record("Rec", "NTNTAGNT", "1!#$12#\""); - - ASSERT_EQ(expected_ntrim, record.trim_trailing_bases(true, 2)); - ASSERT_EQ(expected_record, record); -} - - -TEST(fastq, trim_trailing_bases__trim_mixed__no_low_quality_bases) -{ - const fastq expected_record("Rec", "ACTTAG", "12I$12"); - const fastq::ntrimmed expected_ntrim(0, 0); - fastq record = expected_record; - - ASSERT_EQ(expected_ntrim, record.trim_trailing_bases(true, 2)); - ASSERT_EQ(expected_record, record); -} - - -TEST(fastq, trim_trailing_bases__trim_everything) -{ - fastq record("Rec", "TAG", "!!!"); - const fastq expected_record = fastq("Rec", "", ""); - const fastq::ntrimmed expected_ntrim(0, 3); - ASSERT_EQ(expected_ntrim, record.trim_trailing_bases(true, 2)); - ASSERT_EQ(expected_record, record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// trim_windowed_bases - - -#define PARAMETERIZED_TEST(name, values) \ - class name : public ::testing::TestWithParam {}; \ - INSTANTIATE_TEST_CASE_P(fastq_windowed_trimming, name, values); \ - TEST_P(name, test) - - -// Test for invalid parameters -PARAMETERIZED_TEST(invalid_parameters, ::testing::Values(-1.0, std::numeric_limits::quiet_NaN())) -{ - fastq record("Rec", "TAGTGACAT", "111111111"); - ASSERT_THROW(record.trim_windowed_bases(false, -1, GetParam()), assert_failed); -} - - -// Test for trimming empty reads -PARAMETERIZED_TEST(empty_reads, ::testing::Values(1, 0.1, 3)) -{ - fastq record("Empty", "", ""); - const fastq::ntrimmed expected(0, 0); - ASSERT_EQ(expected, record.trim_windowed_bases(true, 10, GetParam())); - ASSERT_EQ(fastq("Empty", "", ""), record); -} - - -// Test for when entire read is trimmed -PARAMETERIZED_TEST(trim_everything, ::testing::Values(1, 0.2, 4, 10)) -{ - fastq record("Rec", "TAGTGACAT", "111111111"); - const fastq expected_record = fastq("Rec", "", ""); - const fastq::ntrimmed expected_ntrim(9, 0); - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -// Test for when nothing is trimmed -PARAMETERIZED_TEST(trim_nothing, ::testing::Values(0, 1, 0.2, 3, 4, 5, 6, 7, 8, 9, 10, 11)) -{ - fastq record("Rec", "TAGTGACAT", "111111111"); - const fastq expected_record = record; - const fastq::ntrimmed expected_ntrim(0, 0); - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, -1, GetParam())); - ASSERT_EQ(expected_record, record); -} - - -// Test for trimming of Ns -PARAMETERIZED_TEST(trim_ns_1, ::testing::Values(1, 0.2)) -{ - fastq record("Rec", "NNATNT", "234567"); - const fastq expected_record("Rec", "ATNT", "4567"); - const fastq::ntrimmed expected_ntrim(2, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(true, -1, GetParam())); - ASSERT_EQ(expected_record, record); -} - -// - trimming of Ns - the final window contains Ns and is therefore truncated -PARAMETERIZED_TEST(trim_ns_2, ::testing::Values(2, 3, 4)) -{ - fastq record("Rec", "NNATNT", "234567"); - const fastq expected_record("Rec", "AT", "45"); - const fastq::ntrimmed expected_ntrim(2, 2); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(true, -1, GetParam())); - ASSERT_EQ(expected_record, record); -} - -// - trimming of Ns - No valid window is found -TEST(fastq, trim_windowed_bases__trim_ns_5) -{ - fastq record("Rec", "NNATNT", "234567"); - const fastq expected_record("Rec", "", ""); - const fastq::ntrimmed expected_ntrim(6, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(true, -1, 5)); - ASSERT_EQ(expected_record, record); -} - - -// Trimming of 5' only -PARAMETERIZED_TEST(trim_5p_1bp, ::testing::Values(1, 0.1)) -{ - fastq record("Rec", "TAACGATCCG", "0123456789"); - const fastq expected_record("Rec", "CGATCCG", "3456789"); - const fastq::ntrimmed expected_ntrim(3, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -// Trimming of 5' only -PARAMETERIZED_TEST(trim_5p_2bp, ::testing::Values(2, 0.2)) -{ - fastq record("Rec", "TAACGATCCG", "0123456789"); - const fastq expected_record("Rec", "CGATCCG", "3456789"); - const fastq::ntrimmed expected_ntrim(3, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - - -// Trimming of 5' only - lowquality is inclusive -PARAMETERIZED_TEST(trim_5p_inclusive_low_quality, ::testing::Values(2, 3)) -{ - fastq record("Rec", "TAACGATCCG", "0123126789"); - const fastq expected_record("Rec", "TCCG", "6789"); - const fastq::ntrimmed expected_ntrim(6, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -// Trimming of 3' only - lowquality is inclusive -PARAMETERIZED_TEST(trim_3p_inclusive_low_quality, ::testing::Values(3)) -{ - fastq record("Rec", "TAACGATCCG", "9876312333"); - const fastq expected_record("Rec", "TAACG", "98763"); - const fastq::ntrimmed expected_ntrim(0, 5); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -PARAMETERIZED_TEST(tiny_and_huge_window_sizes_1, ::testing::Values(0, 0.01, 20)) -{ - fastq record("Rec", "TAACGATC", "23456789"); - const fastq expected_record("Rec", "", ""); - const fastq::ntrimmed expected_ntrim(8, 0); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '2' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -PARAMETERIZED_TEST(tiny_and_huge_window_sizes_2, ::testing::Values(0, 0.01, 20)) -{ - fastq record("Rec", "TAACGATC", "23456780"); - const fastq expected_record("Rec", "TAACGAT", "2345678"); - const fastq::ntrimmed expected_ntrim(0, 1); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '1' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -PARAMETERIZED_TEST(last_trailing_window, ::testing::Values(1, 2, 3, 4, 5, 6, 7, 8, 9)) -{ - fastq record("Rec", "TAACGATCC", "234567811"); - const fastq expected_record("Rec", "TAACGAT", "2345678"); - const fastq::ntrimmed expected_ntrim(0, 2); - - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(false, '1' - '!', - GetParam())); - ASSERT_EQ(expected_record, record); -} - - -TEST(fastq, trim_windowed_bases__trim_window) -{ - // Should trim starting at the window of low quality bases in the middle - // even with high qual bases at the end. - fastq record("Rec", "NNAAAAAAAAATNNNNNNNA", "##EEEEEEEEEE#######E"); - const fastq expected_record = fastq("Rec", "AAAAAAAAAT", "EEEEEEEEEE"); - const fastq::ntrimmed expected_ntrim(2, 8); - ASSERT_EQ(expected_ntrim, record.trim_windowed_bases(true, 10, 5)); - ASSERT_EQ(expected_record, record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Truncate - -TEST(fastq, truncate_empty) -{ - fastq record("Empty", "", ""); - record.truncate(0, 10); - ASSERT_EQ(fastq("Empty", "", ""), record); -} - - -TEST(fastq, truncate_zero_bases) -{ - const fastq expected_record("Rec", "ACTTAG", "12I$12"); - fastq current_record = expected_record; - current_record.truncate(); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_all_bases) -{ - const fastq expected_record("Rec", "", ""); - fastq current_record("Rec", "ACTTAG", "12I$12"); - current_record.truncate(1, 0); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_5p) -{ - const fastq expected_record("Rec", "TTAG", "I$12"); - fastq current_record("Rec", "ACTTAG", "12I$12"); - current_record.truncate(2); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_3p) -{ - const fastq expected_record("Rec", "ACT", "12I"); - fastq current_record("Rec", "ACTTAG", "12I$12"); - current_record.truncate(0, 3); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_middle) -{ - const fastq expected_record("Rec", "TTA", "I$1"); - fastq current_record("Rec", "ACTTAG", "12I$12"); - current_record.truncate(2, 3); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_len_higher_than_n_bases) -{ - const fastq expected_record("Rec", "TTAG", "I$12"); - fastq current_record("Rec", "ACTTAG", "12I$12"); - current_record.truncate(2, 1024); - ASSERT_EQ(expected_record, current_record); -} - - -TEST(fastq, truncate_pos_after_last_base) -{ - // Same behavior as string::substr - fastq current_record("Rec", "ACTTAG", "12I$12"); - ASSERT_NO_THROW(current_record.truncate(6)); - ASSERT_THROW(current_record.truncate(7), std::out_of_range); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Reverse complement - -TEST(fastq, reverse_complement__empty) -{ - const fastq expected = fastq("Empty", "", ""); - fastq result = fastq("Empty", "", ""); - result.reverse_complement(); - ASSERT_EQ(expected, result); -} - - -TEST(fastq, reverse_complement) -{ - const fastq expected = fastq("Rec", "TACAGANGTN", "0123456789"); - fastq result = fastq("Rec", "NACNTCTGTA", "9876543210"); - result.reverse_complement(); - ASSERT_EQ(expected, result); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Adding prefixes to the header - -TEST(fastq, add_prefix_to_header) -{ - const fastq expected("not_my_header", "ACGTA", "12345"); - fastq record("my_header", "ACGTA", "12345"); - record.add_prefix_to_header("not_"); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, add_prefix_to_header__empty_prefix) -{ - const fastq expected("my_header", "ACGTA", "12345"); - fastq record = expected; - record.add_prefix_to_header(""); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, add_prefix_to_header__header) -{ - const fastq expected("new_header", "ACGTA", "12345"); - fastq record("", "ACGTA", "12345"); - record.add_prefix_to_header("new_header"); - ASSERT_EQ(expected, record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Adding postfixes to the header - -TEST(fastq, add_postfix_to_header) -{ - const fastq expected("my_header new postfix", "ACGTA", "12345"); - fastq record("my_header", "ACGTA", "12345"); - record.add_postfix_to_header(" new postfix"); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, add_postfix_to_header__empty_prefix) -{ - const fastq expected("my_header", "ACGTA", "12345"); - fastq record = expected; - record.add_postfix_to_header(""); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, add_postfix_to_header__header) -{ - const fastq expected("new_header", "ACGTA", "12345"); - fastq record("", "ACGTA", "12345"); - record.add_postfix_to_header("new_header"); - ASSERT_EQ(expected, record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Discarding read, setting seq to N and qual to '!' - -TEST(fastq, discard_read) -{ - const fastq expected("my_header", "N", "!"); - fastq record("my_header", "ACGTA", "12345"); - record.discard(); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, discard_discarded_read) -{ - const fastq expected("my_header", "N", "!"); - fastq record("my_header", "N", "!"); - record.discard(); - ASSERT_EQ(expected, record); -} - - -TEST(fastq, discard_empty_read) -{ - const fastq expected("my_header", "N", "!"); - fastq record("my_header", "", ""); - record.discard(); - ASSERT_EQ(expected, record); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Reading from stream - -TEST(fastq, simple_fastq_record_1) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back("ACGAGTCA"); - lines.push_back("+"); - lines.push_back("!7BF8DGI"); - vec_reader reader(lines); - - fastq record; - ASSERT_TRUE(record.read(reader, FASTQ_ENCODING_33)); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); -} - -TEST(fastq, simple_fastq_record_2) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back("ACGAGTCA"); - lines.push_back("+"); - lines.push_back("!7BF8DGI"); - lines.push_back("@record_2"); - lines.push_back("GTCAGGAT"); - lines.push_back("+"); - lines.push_back("D7BIG!F8"); - vec_reader reader(lines); - - fastq record; - ASSERT_TRUE(record.read(reader, FASTQ_ENCODING_33)); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); - ASSERT_TRUE(record.read(reader, FASTQ_ENCODING_33)); - ASSERT_EQ("record_2", record.header()); - ASSERT_EQ("GTCAGGAT", record.sequence()); - ASSERT_EQ("D7BIG!F8", record.qualities()); - ASSERT_FALSE(record.read(reader, FASTQ_ENCODING_33)); -} - - -TEST(fastq, simple_fastq_record__with_extra_header_1) -{ - string_vec lines; - lines.push_back("@record_1 Extra header here"); - lines.push_back("ACGAGTCA"); - lines.push_back("+"); - lines.push_back("!7BF8DGI"); - vec_reader reader(lines); - - fastq record; - ASSERT_TRUE(record.read(reader, FASTQ_ENCODING_33)); - ASSERT_EQ("record_1 Extra header here", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); - ASSERT_FALSE(record.read(reader, FASTQ_ENCODING_33)); -} - - -TEST(fastq, simple_fastq_record__with_extra_header_2) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back("ACGAGTCA"); - lines.push_back("+Extra header here"); - lines.push_back("!7BF8DGI"); - vec_reader reader(lines); - - fastq record; - ASSERT_TRUE(record.read(reader, FASTQ_ENCODING_33)); - ASSERT_EQ("record_1", record.header()); - ASSERT_EQ("ACGAGTCA", record.sequence()); - ASSERT_EQ("!7BF8DGI", record.qualities()); - ASSERT_FALSE(record.read(reader, FASTQ_ENCODING_33)); -} - - -TEST(fastq, simple_fastq_record__no_header) -{ - string_vec lines; - lines.push_back("@"); - lines.push_back("ACGAGTCA"); - lines.push_back("+"); - lines.push_back("!7BF8DGI"); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader, FASTQ_ENCODING_33), fastq_error); -} - - -TEST(fastq, simple_fastq_record__no_sequence) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back(""); - lines.push_back("+"); - lines.push_back("!7BF8DGI"); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader, FASTQ_ENCODING_33), fastq_error); -} - - -TEST(fastq, simple_fastq_record__no_qualities) -{ - string_vec lines; - lines.push_back("@"); - lines.push_back("ACGAGTCA"); - lines.push_back("+"); - lines.push_back(""); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader, FASTQ_ENCODING_33), fastq_error); -} - - -TEST(fastq, simple_fastq_record__no_qualities_or_sequence) -{ - string_vec lines; - lines.push_back("@"); - lines.push_back(""); - lines.push_back("+"); - lines.push_back(""); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader, FASTQ_ENCODING_33), fastq_error); -} - - -TEST(fastq, eof_when_starting_to_read_record) -{ - string_vec lines; - vec_reader reader(lines); - - fastq record; - ASSERT_FALSE(record.read(reader)); -} - - -TEST(fastq, eof_after_header) -{ - string_vec lines; - lines.push_back("@record"); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_sequence_1) -{ - string_vec lines; - lines.push_back("@record"); - lines.push_back("ACGTA"); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_sequence_2) -{ - string_vec lines; - lines.push_back("@record"); - lines.push_back("ACGTA"); - lines.push_back(""); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_sep_1) -{ - string_vec lines; - lines.push_back("@record"); - lines.push_back("ACGTA"); - lines.push_back("+"); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_sep_2) -{ - string_vec lines; - lines.push_back("@record"); - lines.push_back("ACGTA"); - lines.push_back("+"); - lines.push_back(""); - vec_reader reader(lines); - - fastq record; - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_qualities_following_previous_read_1) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back("ACGTA"); - lines.push_back("+"); - lines.push_back("!!!!!"); - lines.push_back("@record_2"); - lines.push_back("ACGTA"); - lines.push_back("+"); - vec_reader reader(lines); - - fastq record; - ASSERT_NO_THROW(record.read(reader)); - ASSERT_THROW(record.read(reader), fastq_error); -} - - -TEST(fastq, eof_after_qualities_following_previous_read_2) -{ - string_vec lines; - lines.push_back("@record_1"); - lines.push_back("ACGTA"); - lines.push_back("+"); - lines.push_back("!!!!!"); - lines.push_back("@record_2"); - lines.push_back("ACGTA"); - lines.push_back("+"); - lines.push_back(""); - vec_reader reader(lines); - - fastq record; - ASSERT_NO_THROW(record.read(reader)); - ASSERT_THROW(record.read(reader), fastq_error); -} - -/////////////////////////////////////////////////////////////////////////////// -// Writing to stream - -TEST(fastq, Writing_to_stream_phred_33) -{ - const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); - ASSERT_EQ("@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n", record.to_str()); -} - -TEST(fastq, Writing_to_stream_phred_33_explicit) -{ - const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); - ASSERT_EQ("@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n", record.to_str()); -} - -TEST(fastq, Writing_to_stream_phred_64_explicit) -{ - const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); - ASSERT_EQ("@record_1\nACGTACGATA\n+\n@CBCIUWbfi\n", record.to_str(FASTQ_ENCODING_64)); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Validating pairs - -TEST(fastq, validate_paired_reads__throws_if_order_or_number_is_wrong) -{ - const fastq ref_mate0 = fastq("Mate/0", "ACGT", "!!#$"); - const fastq ref_mate1 = fastq("Mate/1", "ACGT", "!!#$"); - const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); - const fastq ref_mate3 = fastq("Mate/3", "ACGT", "!!#$"); - const fastq ref_matea = fastq("Mate/A", "ACGT", "!!#$"); - const fastq ref_mateb = fastq("Mate/B", "ACGT", "!!#$"); - - { - fastq mate0 = ref_mate0; - fastq mate1 = ref_mate1; - ASSERT_THROW(fastq::validate_paired_reads(mate0, mate1), fastq_error); - } - - { - fastq mate0 = ref_mate0; - fastq mate1 = ref_mate1; - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate0), fastq_error); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - fastq::validate_paired_reads(mate1, mate2); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate1), fastq_error); - } - - { - fastq mate2 = ref_mate2; - fastq mate3 = ref_mate3; - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate3), fastq_error); - } - - { - fastq mate2 = ref_mate2; - fastq mate3 = ref_mate3; - ASSERT_THROW(fastq::validate_paired_reads(mate3, mate2), fastq_error); - } - - { - fastq matea = ref_matea; - fastq mateb = ref_mateb; - ASSERT_THROW(fastq::validate_paired_reads(matea, mateb), fastq_error); - } - - { - fastq matea = ref_matea; - fastq mateb = ref_mateb; - ASSERT_THROW(fastq::validate_paired_reads(mateb, matea), fastq_error); - } -} - - -TEST(fastq, validate_paired_reads__allows_other_separators) -{ - const fastq ref_mate1 = fastq("Mate:1", "ACGT", "!!#$"); - const fastq ref_mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - fastq::validate_paired_reads(mate1, mate2, ':'); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate1), fastq_error); - } -} - - -TEST(fastq, validate_paired_reads__mate_separator_is_updated) -{ - const fastq ref_mate_1 = fastq("Mate/1", "ACGT", "!!#$"); - const fastq ref_mate_2 = fastq("Mate/2", "GCTAA", "$!@#$"); - - fastq mate1 = fastq("Mate:1", "ACGT", "!!#$"); - fastq mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); - fastq::validate_paired_reads(mate1, mate2, ':'); - - ASSERT_EQ(mate1, ref_mate_1); - ASSERT_EQ(mate2, ref_mate_2); -} - - -TEST(fastq, validate_paired_reads__throws_if_mate_is_empty) -{ - const fastq ref_mate1 = fastq("Mate", "", ""); - const fastq ref_mate2 = fastq("Mate", "ACGT", "!!#$"); - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate1), fastq_error); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate1), fastq_error); - } -} - - -TEST(fastq, validate_paired_reads__throws_if_only_mate_1_is_numbered) -{ - const fastq ref_mate2 = fastq("Mate/1", "GCTAA", "$!@#$"); - const fastq ref_mate1 = fastq("Mate", "ACGT", "!!#$"); - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate1), fastq_error); - } -} - - -TEST(fastq, validate_paired_reads__throws_if_only_mate_2_is_numbered) -{ - const fastq ref_mate1 = fastq("Mate", "GCTAA", "$!@#$"); - const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); - } - - { - fastq mate1 = ref_mate1; - fastq mate2 = ref_mate2; - ASSERT_THROW(fastq::validate_paired_reads(mate2, mate1), fastq_error); - } -} - - -TEST(fastq, validate_paired_reads__throws_if_mate_is_misnumbered) -{ - fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); - fastq mate2 = fastq("Mate/3", "ACGT", "!!#$"); - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); -} - - -TEST(fastq, validate_paired_reads__throws_if_same_mate_numbers) -{ - fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); - fastq mate2 = fastq("Mate/1", "ACGT", "!!#$"); - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); -} - - -TEST(fastq, validate_paired_reads__throws_if_name_differs) -{ - fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); - fastq mate2 = fastq("WrongName/2", "ACGT", "!!#$"); - ASSERT_THROW(fastq::validate_paired_reads(mate1, mate2), fastq_error); -} - -} // namespace ar diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 TGAGTCAT GTTAGTGG +sample_2 GCAGAGAT CCTAGGGT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +GCAGAGATACCCTAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +GCAGAGATCCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTACACCCTAGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +TGAGTCATCCACTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +TGAGTCATGCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACCCCACTAACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TGAGTCATACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +GCAGAGATGCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGAGTCATAGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +GCAGAGATTAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +CCTAGGGTATCTCTGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +CCTAGGGTGTACCGACAAGCCATTAAGTCAACTCAGCGGAAGTCGTCGGGACGATGCCCAAACGCGCACTTAACTTTTGTAGGATCTCTGCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +GTTAGTGGATGACTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTTAGTGGGGTGATGATATCAGGAGCCGTATTCTAAAGTGATTAGACAATTACATGGACAGACAAACGGCAGTGTAACTGTGCATGACTCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +GTTAGTGGGATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +CCTAGGGTTTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTTAGTGGATGTGGTTATAGCAACCGCTCACTTCTCACGTACTGGTGATACTCCTTTGGTACTTTCAACCGTTTTTCCTTTTACGAGATAATCTGGATGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +CCTAGGGTCCTCTCGATTCGGCAGTACCCAATTGTTGACGATCAGCATATTATTATCTGATTGTGCTCGGCGCCCTACATTTCGCGTTGGAGTGTACGCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_read_s1_075 +GCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACC ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ +@M_read_s1_150 +AGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTTGAAAGTACCAAAGGAGTATCACCAGTACGTGAGAAGTGAGCGGTTGCTATAACCACAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_000 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_200/1 +ACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_200/2 +GATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,210 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* TGAGTCAT GTTAGTGG +sample_2 GCAGAGAT CCTAGGGT + + +[Adapter sequences] +Adapter1[1]: CCACTAAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGACTCA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4078236736 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of full-length collapsed pairs: 2 +Number of truncated collapsed pairs: 0 +Number of retained reads: 4 +Number of retained nucleotides: 409 +Average length of retained reads: 102.25 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 1 0 0 1 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 1 1 0 0 0 0 2 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_read_s2_075 +CCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTAC ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ +@M_read_s2_150 +TAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGAGCACAATCAGATAATAATATGCTGATCGTCAACAATTGGGTACTGCCGAATCGAGAGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_000 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_200/1 +GCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_200/2 +TTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,210 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TGAGTCAT GTTAGTGG +sample_2* GCAGAGAT CCTAGGGT + + +[Adapter sequences] +Adapter1[1]: ACCCTAGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATCTCTGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4078236736 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of full-length collapsed pairs: 2 +Number of truncated collapsed pairs: 0 +Number of retained reads: 4 +Number of retained nucleotides: 409 +Average length of retained reads: 102.25 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 1 0 0 1 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 1 1 0 0 0 0 2 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TGAGTCAT GTTAGTGG +sample_2 GCAGAGAT CCTAGGGT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 TGAGTCAT GTTAGTGG 4 0.500 +sample_2 GCAGAGAT CCTAGGGT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +N ++ +! +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/2 +N ++ +! +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/combined_output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_150/1 +TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2* AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,28 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GGCCCCTG CCAAAGCT 4 0.500 +sample_2 AATCCTAG GTCTAGTT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_150/1 +TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_150/2 +TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/2 +CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2* AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,28 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GGCCCCTG CCAAAGCT 4 0.500 +sample_2 AATCCTAG GTCTAGTT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_150/1 +TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_150/2 +TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_000/1 +AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_000/2 +CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2* AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,28 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 2 0.250 +ambiguous NA NA 0 0.000 +sample_1 GGCCCCTG CCAAAGCT 3 0.375 +sample_2 AATCCTAG GTCTAGTT 3 0.375 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_200/1 +TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_200/2 +CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 TTTTCAAC TAGATGGC +sample_2 CTTTACAG GGGCTGCT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,64 @@ +@read_s2_000/1 +CTTTACAGAGCAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +GGGCTGCTCTGTAAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TTTTCAACTTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +TAGATGGCGTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CTTTACAGCCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +GGGCTGCTAATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +TTTTCAACTCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCAGCCATCTAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +TAGATGGCTGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGAGTTGAAAAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CTTTACAGCCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGCAGCAGCCCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GGGCTGCTGCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGGCTGTAAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +TTTTCAACGCCATCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +TAGATGGCGTTGAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CTTTACAGTTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GGGCTGCTGTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TTTTCAACCAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +TAGATGGCTAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s1_150/1 +TTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +TCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_075/2 +TGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +CAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +TAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* TTTTCAAC TAGATGGC +sample_2 CTTTACAG GGGCTGCT + + +[Adapter sequences] +Adapter1[1]: GCCATCTA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: GTTGAAAA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s2_200/1 +CCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +AATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_075/2 +GCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +TTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TTTTCAAC TAGATGGC +sample_2* CTTTACAG GGGCTGCT + + +[Adapter sequences] +Adapter1[1]: AGCAGCCC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTGTAAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TTTTCAAC TAGATGGC +sample_2 CTTTACAG GGGCTGCT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 TTTTCAAC TAGATGGC 4 0.500 +sample_2 CTTTACAG GGGCTGCT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 TGTAACGC CTCCTTAG +sample_2 GGGGACTC GTATATGC diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_150/1 +TGTAACGCGAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +TGTAACGCCTAAGGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +GGGGACTCAAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGGGCATATACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +GGGGACTCGCATATACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TGTAACGCCCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +TGTAACGCTGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCCCTAAGGAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +GGGGACTCCATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +GGGGACTCATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_150/2 +CTCCTTAGTGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CTCCTTAGGCGTTACAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +GTATATGCCCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTTGAGTCCCCAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +GTATATGCGAGTCCCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CTCCTTAGGTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +CTCCTTAGGGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCAGCGTTACAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +GTATATGCCGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +GTATATGCAGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s1_150/1 +GAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +TGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +GTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +TGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_075/2 +GGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* TGTAACGC CTCCTTAG +sample_2 GGGGACTC GTATATGC + + +[Adapter sequences] +Adapter1[1]: CTAAGGAG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: GCGTTACA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s2_075/1 +AAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_075/2 +CCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +CATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +CGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +ATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +AGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TGTAACGC CTCCTTAG +sample_2* GGGGACTC GTATATGC + + +[Adapter sequences] +Adapter1[1]: GCATATAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: GAGTCCCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 TGTAACGC CTCCTTAG +sample_2 GGGGACTC GTATATGC + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 TGTAACGC CTCCTTAG 4 0.500 +sample_2 GGGGACTC GTATATGC 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/2 +TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/2 +AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/2 +TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/2 +AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,150 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 518 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/pe/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,149 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 935224950 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 2 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 1 1 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 1 0 0 1 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,149 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 935224950 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 2 +Number of reads with adapters[1]: 3 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 1 1 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 1 0 0 1 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 1 0 0 0 1 +92 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4115144913 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 356769071 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +N ++ +! +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/combined_output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4115144913 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 356769071 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_150/1 +TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2* AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,26 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GGCCCCTG CCAAAGCT 4 0.500 +sample_2 AATCCTAG GTCTAGTT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_150/1 +TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2* AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,26 @@ +AdapterRemoval ver. 2.1.7 +Demultiplexing of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GGCCCCTG CCAAAGCT +sample_2 AATCCTAG GTCTAGTT + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 1 0.125 +ambiguous NA NA 0 0.000 +sample_1 GGCCCCTG CCAAAGCT 3 0.375 +sample_2 AATCCTAG GTCTAGTT 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_200/1 +TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,13 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4115144913 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 356769071 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4115144913 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 356769071 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_000/1 +CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2* CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 1 +Number of well aligned reads: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 3 +Number of retained reads: 3 +Number of retained nucleotides: 258 +Average length of retained reads: 86 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 1 0 1 +92 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_200/1 +GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 +@read_s2_075/1 +TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_150/1 +AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/double_indexed/se/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of double-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CTTGCCCT ACGTTATT +sample_2 CGCCGATG TGCACGGG + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CTTGCCCT ACGTTATT 4 0.500 +sample_2 CGCCGATG TGCACGGG 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 CAAGCACG +sample_2 ATTTTGAG diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_200/1 +ATTTTGAGCTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +ATTTTGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +ATTTTGAGGATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +CAAGCACGAAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +ATTTTGAGCTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTTAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/1 +CAAGCACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +CAAGCACGTCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +CAAGCACGTCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCGAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s2_200/2 +ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +CTCAAAATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +ACTATGGTTGTCTGAATCACAAATGGCTAAACGGCTTCATAATAGTGTGGTATGCGTACTAAGTCTGCGGTCCTCACGATGTCACTGTCTACTATTTAGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +AAGGGTTGTGTCAGGGAACCACGATTAGATTCCGTCACGCATGCCCTAAAATGACCAAGAGGAAGTCTTTTCAAGCTCAAAATAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +CGTGCTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +TCGCGCGAACGGCGCTGGGCCCCATGCGAAAAAGCGATACCATGAAGCGAGTATAATGTTCATGCACAGCCGCGATCCGAGCGCCCCACTGCATTGACGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +CGGTTGGGAGCTAGGCATGGGCTGTCTACTTTGTCGTGCCGGGTACCATGTAGGAATTGCCCACCGAGACTACGACGTGCTTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_read_s1_150 +TCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAACATTATACTCGCTTCATGGTATCGCTTTTTCGCATGGGGCCCAGCGCCGTTCGCGCGA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH +@M_read_s1_075 +TCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCG ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_000 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_200/1 +AAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_200/2 +ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,210 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* CAAGCACG * +sample_2 ATTTTGAG * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CGTGCTTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2769367494 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of full-length collapsed pairs: 2 +Number of truncated collapsed pairs: 0 +Number of retained reads: 4 +Number of retained nucleotides: 417 +Average length of retained reads: 104.25 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 1 0 0 1 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 1 0 0 0 0 0 1 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 1 0 0 0 0 1 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_read_s2_150 +GATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAGTACGCATACCACACTATTATGAAGCCGTTTAGCCATTTGTGATTCAGACAACCATAGT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH +@M_read_s2_075 +CTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_000 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_200/1 +CTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_200/2 +ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,210 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CAAGCACG * +sample_2* ATTTTGAG * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: CTCAAAAT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2769367494 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of full-length collapsed pairs: 2 +Number of truncated collapsed pairs: 0 +Number of retained reads: 4 +Number of retained nucleotides: 417 +Average length of retained reads: 104.25 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 1 0 0 1 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 1 0 0 0 0 0 1 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 1 0 0 0 0 1 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 CAAGCACG * +sample_2 ATTTTGAG * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 CAAGCACG * 4 0.500 +sample_2 ATTTTGAG * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/1 +N ++ +! +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/2 +N ++ +! +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +N ++ +! +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/2 +N ++ +! +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/combined_output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/1 +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,19 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/demux_only/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,28 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,64 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,24 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2459456692 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1157297082 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--thread", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/2 +TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/2 +ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 + ++ + +@read_s1_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/2 +GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s1_200/2 +CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/2 +ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_000/1 + ++ + +@read_s2_000/2 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/2 +AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/2 +TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> +@read_s2_200/2 +ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,158 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 4 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 3 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 4 +Number of retained reads: 6 +Number of retained nucleotides: 534 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 1 1 0 0 2 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/pe/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-indexed paired-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 +Maximum mate 1 mismatches: 0 +Maximum mate 2 mismatches: 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,149 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3843883243 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 2 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 1 1 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 1 0 0 1 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,149 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3843883243 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 2 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 1 1 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 1 0 0 1 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/1 +N ++ +! +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +N ++ +! +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/combined_output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s1_000/1 +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_s2_000/1 +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,17 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/demux_only/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,26 @@ +AdapterRemoval ver. 2.2.0 +Demultiplexing of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3717807245 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/barcodes.txt adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/barcodes.txt --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/barcodes.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +sample_1 GCGCCGGA +sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/info.json adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,32 @@ +@read_s1_000/1 +GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_000/1 +CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_075/1 +GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_150/1 +CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_200/1 +GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_200/1 +CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s1_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1* GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s1_075/1 +GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s1_200/1 +TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s1_150/1 +TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@read_s2_000/1 + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2* CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 4 +Number of unaligned reads: 2 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 3 +Number of reads with adapters[1]: 2 +Number of retained reads: 3 +Number of retained nucleotides: 259 +Average length of retained reads: 86.3333 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 1 0 1 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 2 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,12 @@ +@read_s2_150/1 +TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 +@read_s2_075/1 +TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; +@read_s2_200/1 +ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT ++ +GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/demultiplexing/single_indexed/se/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-indexed single-end reads + + +[Demultiplexing] +Maximum mismatches (total): 0 + + +[Demultiplexing samples] +Name Barcode_1 Barcode_2 +sample_1 GCGCCGGA * +sample_2 CAGGACAT * + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Demultiplexing statistics] +Name Barcode_1 Barcode_2 Hits Fraction +unidentified NA NA 0 0.000 +ambiguous NA NA 0 0.000 +sample_1 GCGCCGGA * 4 0.500 +sample_2 CAGGACAT * 4 0.500 +* * * 8 1.000 diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/adapters.txt adapterremoval-2.2.3/tests/regression/misc/adapter_list/adapters.txt --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/adapters.txt 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/adapters.txt 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1 @@ +AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/info.json adapterremoval-2.2.3/tests/regression/misc/adapter_list/info.json --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--adapter-list", "adapters.txt"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/adapter_list/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/input_2.fastq adapterremoval-2.2.3/tests/regression/misc/adapter_list/input_2.fastq --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.settings adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.settings --- adapterremoval-2.2.2/tests/regression/misc/adapter_list/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/adapter_list/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": ["--demultiplex-only"], + "return_code": 1, + "stderr": [ + "Cannot use --demultiplex-only without specifying a list of barcodes using --barcode-list!" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/input_2.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/input_2.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/demux_without_barcodes/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/demux_without_barcodes/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": [], + "return_code": 1, + "stderr": [ + "Error: Different number of files specified for --file1 and --file2." + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_1a.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_1b.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG +@read_150_3/2 +GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT ++ +HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_2b.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_2b.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_2b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/2 +TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA ++ +HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 +@read_150_7/2 +ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT ++ +HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_2c.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_2c.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file1/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file1/input_2c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_150_9/2 +GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT ++ +GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= +@read_150_10/2 +TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": [], + "return_code": 1, + "stderr": [ + "Error: Different number of files specified for --file1 and --file2." + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/input_1a.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/input_1b.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/fewer_file2/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/fewer_file2/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG +@read_150_3/2 +GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT ++ +HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/file2_only/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/file2_only/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/file2_only/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/file2_only/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": [], + "return_code": 1, + "stderr": [ + "Error: Different number of files specified for --file1 and --file2." + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": ["--identify-adapters", "--demultiplex-only"], + "return_code": 1, + "stderr": [ + "Cannot use --identify-adapters and --demultiplex-only at the same time!" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/input_2.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/input_2.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/ident_and_demux/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/ident_and_demux/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/negative_window/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/negative_window/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/negative_window/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/negative_window/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": ["--trimwindows", "-1"], + "return_code": 1, + "stderr": [ + "Error: Invalid value for --trimwindows" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/negative_window/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/negative_window/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/negative_window/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/negative_window/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500_1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500_2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": ["--interleaved"], + "return_code": 1, + "stderr": [ + "Pair contains reads with mismatching names:" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500_1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500_2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved_input/info.json adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved_input/info.json --- adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": ["--interleaved-input"], + "return_code": 1, + "stderr": [ + "Pair contains reads with mismatching names:" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved_input/input_1.fastq adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved_input/input_1.fastq --- adapterremoval-2.2.2/tests/regression/misc/bad_args/se_interleaved_input/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/bad_args/se_interleaved_input/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500_1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500_2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/misc/empty/pe/info.json adapterremoval-2.2.3/tests/regression/misc/empty/pe/info.json --- adapterremoval-2.2.2/tests/regression/misc/empty/pe/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/empty/pe/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/empty/pe/your_output.settings adapterremoval-2.2.3/tests/regression/misc/empty/pe/your_output.settings --- adapterremoval-2.2.2/tests/regression/misc/empty/pe/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/empty/pe/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 220897227 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 0 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All diff -Nru adapterremoval-2.2.2/tests/regression/misc/empty/se/info.json adapterremoval-2.2.3/tests/regression/misc/empty/se/info.json --- adapterremoval-2.2.2/tests/regression/misc/empty/se/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/empty/se/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/misc/empty/se/your_output.settings adapterremoval-2.2.3/tests/regression/misc/empty/se/your_output.settings --- adapterremoval-2.2.2/tests/regression/misc/empty/se/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/empty/se/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,44 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2121675954 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 0 +Number of unaligned reads: 0 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All diff -Nru adapterremoval-2.2.2/tests/regression/misc/no_arguments/info.json adapterremoval-2.2.3/tests/regression/misc/no_arguments/info.json --- adapterremoval-2.2.2/tests/regression/misc/no_arguments/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/misc/no_arguments/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,7 @@ +{ + "arguments": [], + "return_code": 1, + "stderr": [ + "This program searches for" + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,148 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1203911406 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,148 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2579970730 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,148 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2579970730 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2644350168 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2806715714 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3115920885 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2416745148 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2644350168 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2806715714 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3115920885 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2543753157 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 108917414 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 108917414 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2294078498 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2378184469 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 99 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 1 0 1 +100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2394981856 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 99 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 1 0 1 +100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,89 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2027572855 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 1 1 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2010319782 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 1 1 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2024298981 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 1 1 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCATN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCAT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220. diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 196 +Average length of retained reads: 98 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 1 0 0 1 +98 0 0 0 0 0 +99 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3198577441 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 198 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities", "--minquality", "31"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGC ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,114 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3418474566 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 31: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 1 +Number of well aligned read pairs: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 135 +Average length of retained reads: 67.5 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 1 0 0 0 1 +68 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_ATAGCCSeq_1_2959_500 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,198 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 664708214 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 150 +Average length of retained reads: 150 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse-deterministic"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATCGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@C8AA@A@@@?>>@==<=<<;;;<:9777755321/D)'! \ No newline at end of file diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGACTAGCGTGTAGCTTCCAATATGAGGCCGGAATATCAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@<>?@@=>><=;:9:9:9866852220.*&! \ No newline at end of file diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_ATAGCCSeq_1_2959_500 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGNTATTCCGGCCTCATATNGGAAGCTACACGCTAGNCCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJ!JJJJJJJJJJJJJJJJ!JJJJJJJJJJJJJJJJ!JJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/collapse_deterministic/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,198 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 150 +Average length of retained reads: 150 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,198 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1520646958 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 150 +Average length of retained reads: 150 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ +@M_ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,198 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1520646958 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 150 +Average length of retained reads: 150 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 0 0 0 0 +51 0 0 0 0 0 0 0 +52 0 0 0 0 0 0 0 +53 0 0 0 0 0 0 0 +54 0 0 0 0 0 0 0 +55 0 0 0 0 0 0 0 +56 0 0 0 0 0 0 0 +57 0 0 0 0 0 0 0 +58 0 0 0 0 0 0 0 +59 0 0 0 0 0 0 0 +60 0 0 0 0 0 0 0 +61 0 0 0 0 0 0 0 +62 0 0 0 0 0 0 0 +63 0 0 0 0 0 0 0 +64 0 0 0 0 0 0 0 +65 0 0 0 0 0 0 0 +66 0 0 0 0 0 0 0 +67 0 0 0 0 0 0 0 +68 0 0 0 0 0 0 0 +69 0 0 0 0 0 0 0 +70 0 0 0 0 0 0 0 +71 0 0 0 0 0 0 0 +72 0 0 0 0 0 0 0 +73 0 0 0 0 0 0 0 +74 0 0 0 0 0 0 0 +75 0 0 0 0 0 0 0 +76 0 0 0 0 0 0 0 +77 0 0 0 0 0 0 0 +78 0 0 0 0 0 0 0 +79 0 0 0 0 0 0 0 +80 0 0 0 0 0 0 0 +81 0 0 0 0 0 0 0 +82 0 0 0 0 0 0 0 +83 0 0 0 0 0 0 0 +84 0 0 0 0 0 0 0 +85 0 0 0 0 0 0 0 +86 0 0 0 0 0 0 0 +87 0 0 0 0 0 0 0 +88 0 0 0 0 0 0 0 +89 0 0 0 0 0 0 0 +90 0 0 0 0 0 0 0 +91 0 0 0 0 0 0 0 +92 0 0 0 0 0 0 0 +93 0 0 0 0 0 0 0 +94 0 0 0 0 0 0 0 +95 0 0 0 0 0 0 0 +96 0 0 0 0 0 0 0 +97 0 0 0 0 0 0 0 +98 0 0 0 0 0 0 0 +99 0 0 0 0 0 0 0 +100 0 0 0 0 0 0 0 +101 0 0 0 0 0 0 0 +102 0 0 0 0 0 0 0 +103 0 0 0 0 0 0 0 +104 0 0 0 0 0 0 0 +105 0 0 0 0 0 0 0 +106 0 0 0 0 0 0 0 +107 0 0 0 0 0 0 0 +108 0 0 0 0 0 0 0 +109 0 0 0 0 0 0 0 +110 0 0 0 0 0 0 0 +111 0 0 0 0 0 0 0 +112 0 0 0 0 0 0 0 +113 0 0 0 0 0 0 0 +114 0 0 0 0 0 0 0 +115 0 0 0 0 0 0 0 +116 0 0 0 0 0 0 0 +117 0 0 0 0 0 0 0 +118 0 0 0 0 0 0 0 +119 0 0 0 0 0 0 0 +120 0 0 0 0 0 0 0 +121 0 0 0 0 0 0 0 +122 0 0 0 0 0 0 0 +123 0 0 0 0 0 0 0 +124 0 0 0 0 0 0 0 +125 0 0 0 0 0 0 0 +126 0 0 0 0 0 0 0 +127 0 0 0 0 0 0 0 +128 0 0 0 0 0 0 0 +129 0 0 0 0 0 0 0 +130 0 0 0 0 0 0 0 +131 0 0 0 0 0 0 0 +132 0 0 0 0 0 0 0 +133 0 0 0 0 0 0 0 +134 0 0 0 0 0 0 0 +135 0 0 0 0 0 0 0 +136 0 0 0 0 0 0 0 +137 0 0 0 0 0 0 0 +138 0 0 0 0 0 0 0 +139 0 0 0 0 0 0 0 +140 0 0 0 0 0 0 0 +141 0 0 0 0 0 0 0 +142 0 0 0 0 0 0 0 +143 0 0 0 0 0 0 0 +144 0 0 0 0 0 0 0 +145 0 0 0 0 0 0 0 +146 0 0 0 0 0 0 0 +147 0 0 0 0 0 0 0 +148 0 0 0 0 0 0 0 +149 0 0 0 0 0 0 0 +150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1638235704 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2898275634 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1902493234 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4016683054 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1638235704 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2898275634 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1902493234 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 1 1 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "100", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4016683054 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 100 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 11384421 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 11384421 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of interleaved paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 36753401 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/interleaved/output/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 32142888 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2714819290 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3802049955 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 99 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 1 0 1 +100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "99", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3867243128 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 99 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 99 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 1 0 1 +100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "90", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,135 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4291984462 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 90 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 1 1 +89 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "90", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4294353461 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 90 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 1 1 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "90", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1485681 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 90 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 1 1 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 242897042 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 200 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGNNNNNNNNNNNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCNNNNNNN ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<: diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGC ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,139 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 236123159 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 178 +Average length of retained reads: 89 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 1 0 0 0 1 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 727785539 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 198 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/info.json adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/info.json --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities", "--minquality", "31"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCT ++ +JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B diff -Nru adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,113 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 737094053 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 31: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 2 +Number of retained nucleotides: 134 +Average length of retained reads: 67 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,98 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@MT_AAGGGCSeq_1_5180_50 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/collapse_truncated/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,97 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 505768950 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 1 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,98 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@MT_AAGGGCSeq_1_5180_50/1 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@MT_AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,97 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 505768950 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 1 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ +@M_AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,98 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 0 0 0 +50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--trimns", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@MT_AAGGGCSeq_1_5180_50/1 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ +@MT_AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,97 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 505768950 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 1 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 0 0 0 0 +39 0 0 0 0 0 0 0 +40 0 0 0 0 0 0 0 +41 0 0 0 0 0 0 0 +42 0 0 0 0 0 0 0 +43 0 0 0 0 0 0 0 +44 0 0 0 0 0 0 0 +45 0 0 0 0 0 0 0 +46 0 0 0 0 0 0 0 +47 0 0 0 0 0 0 0 +48 0 0 0 0 0 0 0 +49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC +@AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3738807510 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +N ++ +! +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3854997780 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +N ++ +! +@AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3934188119 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3738807510 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3854997780 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--trimns", "--minlength", "50"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/combined_output/keep_neither/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3934188119 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "49"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1200660835 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 49 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "49", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1359054103 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 49 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 1 0 1 +50 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "49", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1361295368 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 49 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 1 0 1 +50 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/both/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1436203328 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1647601792 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 1 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "50", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +NGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +GGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +IHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1757553206 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 50 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 1 1 +50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD +@read_150_10/1 +TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT ++ +<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2a.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_1/2 +AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC ++ +HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>E6,735@GG +@read_150_3/2 +GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT ++ +HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2b.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/2 +TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA ++ +HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 +@read_150_7/2 +ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT ++ +HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2c.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/input_2c.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@read_150_9/2 +GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT ++ +GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= +@read_150_10/2 +TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,40 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD +@read_150_10/1 +TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT ++ +<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,40 @@ +@read_150_1/2 +AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC ++ +HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 +@read_150_5/2 +TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA ++ +HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 +@read_150_7/2 +ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT ++ +HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B +@read_150_9/2 +GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT ++ +GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= +@read_150_10/2 +TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,146 @@ +AdapterRemoval ver. 2.2.0 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4274826581 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 10 +Number of unaligned read pairs: 4 +Number of well aligned read pairs: 6 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 20 +Number of retained nucleotides: 1970 +Average length of retained reads: 98.5 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 1 1 0 0 2 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 9 9 0 0 18 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/excl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2986012581 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBE diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimns/incl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3028896355 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 93 +Average length of retained reads: 46.5 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 1 0 0 1 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/default/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3078066396 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 100 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/info.json adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/info.json --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities", "--minquality", "35"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDE diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.settings adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/incl_adapter/trimqualities/minq35/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3153498613 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 35: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 97 +Average length of retained reads: 48.5 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 1 0 0 0 1 +49 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_CTTTGTSeq_1_14286_0 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 416750178 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_CTTTGTSeq_1_14286_0/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_CTTTGTSeq_1_14286_0/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,48 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 416750178 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/combined_output/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/combined_output/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,46 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 688407609 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + +@CTTTGTSeq_1_14286_0/2 data meta + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,46 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 861004460 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/your_output.discarded adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/your_output.discarded --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,8 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + +@CTTTGTSeq_1_14286_0/2 data meta + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,46 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 861004460 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/info.json adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/info.json --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "0"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta +AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ++ +JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/2 data meta + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.settings adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/only_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/only_adapter/minlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,46 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 934075502 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 0 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim3p", "6"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFF diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBE diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 6 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 88 +Average length of retained reads: 44 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim3p", "3", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFED diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/3p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/3p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 3 1 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 96 +Average length of retained reads: 48 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 1 0 0 0 1 +48 0 0 0 0 0 +49 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "8"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +AACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +TAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,88 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 8 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 84 +Average length of retained reads: 42 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "1", "--trim3p", "4"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAG ++ +JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFE diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +GGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTC ++ +IHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDF diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,91 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 1 +Trimming 3p: 4 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 90 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "1", "3", "--trim3p", "4", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAG ++ +JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFE diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +CCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCAT ++ +JJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFED diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_and_3p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,91 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 1 3 +Trimming 3p: 4 2 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 90 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "5", "7"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.pair1.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.pair1.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.pair1.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.pair2.truncated adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.pair2.truncated --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.pair2.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +CTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT ++ +JJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/5p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/5p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,91 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 372265332 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 5 7 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of retained reads: 2 +Number of retained nucleotides: 88 +Average length of retained reads: 44 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 1 0 0 1 +44 0 0 0 0 0 +45 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trim5p", "6"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50 meta data +CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGG ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ& diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,86 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 6 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 38 +Average length of retained reads: 38 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trim5p", "6", "--trim3p", "20"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50 meta data +CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGG ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ& diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_and_3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,86 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 6 +Trimming 3p: 20 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 38 +Average length of retained reads: 38 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 0 0 0 0 +37 0 0 0 0 0 0 0 +38 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/info.json adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trim5p", "6", "8"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/input_2.fastq adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/input_2.fastq --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/2 data meta +AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC ++ +JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.collapsed adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50 meta data +CTAACACCCTTAATTCCATCCACCCTCCTCTCCCTA ++ +JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ diff -Nru adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/pe/trimfixed/collapse_5p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,84 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 429139444 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 6 8 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of discarded mate 2 reads: 0 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 2 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 36 +Average length of retained reads: 36 + + +[Length distribution] +Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 0 0 +1 0 0 0 0 0 0 0 +2 0 0 0 0 0 0 0 +3 0 0 0 0 0 0 0 +4 0 0 0 0 0 0 0 +5 0 0 0 0 0 0 0 +6 0 0 0 0 0 0 0 +7 0 0 0 0 0 0 0 +8 0 0 0 0 0 0 0 +9 0 0 0 0 0 0 0 +10 0 0 0 0 0 0 0 +11 0 0 0 0 0 0 0 +12 0 0 0 0 0 0 0 +13 0 0 0 0 0 0 0 +14 0 0 0 0 0 0 0 +15 0 0 0 0 0 0 0 +16 0 0 0 0 0 0 0 +17 0 0 0 0 0 0 0 +18 0 0 0 0 0 0 0 +19 0 0 0 0 0 0 0 +20 0 0 0 0 0 0 0 +21 0 0 0 0 0 0 0 +22 0 0 0 0 0 0 0 +23 0 0 0 0 0 0 0 +24 0 0 0 0 0 0 0 +25 0 0 0 0 0 0 0 +26 0 0 0 0 0 0 0 +27 0 0 0 0 0 0 0 +28 0 0 0 0 0 0 0 +29 0 0 0 0 0 0 0 +30 0 0 0 0 0 0 0 +31 0 0 0 0 0 0 0 +32 0 0 0 0 0 0 0 +33 0 0 0 0 0 0 0 +34 0 0 0 0 0 0 0 +35 0 0 0 0 0 0 0 +36 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/README adapterremoval-2.2.3/tests/regression/README --- adapterremoval-2.2.2/tests/regression/README 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/README 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,60 @@ +Sequences: + No adapter + Short adapter + Long adapter + Complete adapter + +Filetypes: + Unix + Windows (\r\n) + + +Automatic variants? + - gzip + - bzip + - uncompressed + + +Single end: +x --collapse +x --combined-output +x --trimns +x --trimqualities +x --minlength +x --maxlength + + Bad: + --interleaved + --interleaved-input + --interleaved-output + + + + + + + + + +Possibilities: + - adapter + - overlap + - collapse (yes, no, yes but too short) + - lq trimming + + + +TODO: + - Single-end + - No adapter + - No adapter, lq trimming + + + - Single-end + - No adapter + - No adapter, lq trimming + - No adapter, overlapping + - No adapter, overlapping, lq trimming + - No adapter, overlapping, too short + - No adapter, overlapping, too short, lq trimming + diff -Nru adapterremoval-2.2.2/tests/regression/run adapterremoval-2.2.3/tests/regression/run --- adapterremoval-2.2.2/tests/regression/run 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/run 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,515 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- +# Copyright (c) 2016 Mikkel Schubert +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. +from __future__ import print_function + +import argparse +import bz2 +import cStringIO +import difflib +import gzip +import json +import os +import re +import subprocess +import sys +import tempfile +import types + + +############################################################################# +_COLORS_ENABLED = True + + +def _do_print_color(*vargs, **kwargs): + """Utility function: Prints using shell colors.""" + colorcode = kwargs.pop("colorcode") + destination = kwargs.pop("file", sys.stdout) + + # No colors if output is redirected (e.g. less, file, etc.) + if _COLORS_ENABLED and destination.isatty(): + vargs = list(vargs) + for (index, varg) in enumerate(vargs): + varg_lines = [] + # Newlines terminate the color-code for e.g. 'less', so ensure that + # each line is color-coded, while preserving the list of arguments + for line in str(varg).split("\n"): + varg_lines.append("\033[00;%im%s\033[00m" % (colorcode, line)) + vargs[index] = "\n".join(varg_lines) + + print(*vargs, file=destination, **kwargs) + + if '\n' in kwargs.get('end', '\n'): + destination.flush() + + +def print_ok(*vargs, **kwargs): + """Equivalent to print, but prints using shell colorcodes (green).""" + _do_print_color(*vargs, colorcode=32, **kwargs) + + +def print_err(*vargs, **kwargs): + """Equivalent to print, but prints using shell colorcodes (red).""" + _do_print_color(*vargs, colorcode=31, **kwargs) + + +############################################################################# +UNCOMPRESSED, GZIP, BZIP2 = "raw", "gz", "bz2" + + +def compress(value, compression): + fileobj = cStringIO.StringIO() + + if compression == GZIP: + handle = gzip.GzipFile('', 'w', 9, fileobj) + handle.write(value) + handle.close() + + return fileobj.getvalue() + elif compression == BZIP2: + return bz2.compress(value) + else: + assert False, compression + + +def decompress(filename): + with open(filename) as handle: + value = handle.read() + + if value and filename.endswith(".bz2"): + if not value.startswith("BZ"): + raise TestError("Expected bz2 file at %r, but header is %r" + % (filename, value[:2])) + + value = bz2.decompress(value) + elif value and filename.endswith(".gz"): + if not value.startswith("\x1f\x8b"): + raise TestError("Expected gzip file at %r, but header is %r" + % (filename, value[:2])) + + fileobj = cStringIO.StringIO(value) + handle = gzip.GzipFile('', 'r', 9, fileobj) + + value = handle.read() + + return cStringIO.StringIO(value).readlines() + + +############################################################################# +_EXEC = './build/AdapterRemoval' +_INFO_FILE = "info.json" +_INFO_FIELDS = { + 'arguments': types.ListType, + 'return_code': types.IntType, + 'stderr': types.ListType, +} + + +def pretty_output(s, padding=0, max_lines=float("inf")): + padding = " " * padding + lines = s.split("\n") + if len(lines) > max_lines: + lines = lines[:max_lines] + lines.append("...") + + result = [] + for line in lines: + result.append("%s> %s" % (padding, line)) + + return "\n".join(result) + + +def interleave(texts_1, texts_2): + files = [] + + for text_1, text_2 in zip(texts_1, texts_2): + lines_1 = text_1.split("\n") + lines_2 = text_2.split("\n") + iters = (iter(lines_1).next, iter(lines_2).next) + + assert len(lines_1) == len(lines_2) + + result = [] + while True: + try: + for it in iters: + for _ in xrange(4): + result.append(it()) + except StopIteration: + break + + files.append("\n".join(result)) + + return files + + +class TestError(StandardError): + pass + + +class TestCase(object): + def __init__(self, root, path): + self.root = root + self.path = path + self.name = " :: ".join(path) + self._files = self._collect_files(root) + self._info = self._read_info(os.path.join(root, _INFO_FILE)) + + def __repr__(self): + return "TestCase(%r)" % ({'root': self.root, + 'name': self.name, + 'info': self._info, + 'files': self._files}) + + def run(self, root): + root = os.path.join(root, *self.path) + + interleaved_tests = [False] + if self._is_properly_paired(): + interleaved_tests.append(True) + + for in_compression in (UNCOMPRESSED, GZIP, BZIP2): + for out_compression in (UNCOMPRESSED, GZIP, BZIP2): + for interleaved in interleaved_tests: + yield "%s>%s%s" % (in_compression, + out_compression, + ",intl" if interleaved else "") + + postfix = "%s_%s%s" % (in_compression, + out_compression, + "_intl" if interleaved else "") + + self._do_run(os.path.join(root, postfix), + in_compression, out_compression, interleaved) + + def _do_run(self, root, in_compression=UNCOMPRESSED, + out_compression=UNCOMPRESSED, interleaved=False): + assert in_compression in (UNCOMPRESSED, BZIP2, GZIP) + assert out_compression in (UNCOMPRESSED, BZIP2, GZIP) + os.makedirs(root) + + input_1, input_2 = self._setup_input(root, in_compression, interleaved) + self._do_call(root, input_1, input_2, out_compression, interleaved) + + self._check_file_creation(root, input_1, input_2, out_compression) + self._check_file_contents(root, out_compression) + + def _setup_input(self, root, compression, interleaved): + input_files = {} + for key in ("input_1", "input_2"): + input_files[key] = [open(filename).read() + for filename in self._files[key]] + + if interleaved: + input_files = {"input_1": interleave(input_files["input_1"], + input_files["input_2"]), + "input_2": []} + + final_files = {} + for key, values in input_files.iteritems(): + filenames = [] + for idx, value in enumerate(values): + filename = '%s%s.fastq' % (key, chr(ord('a') + idx)) + if compression != UNCOMPRESSED: + filename += "." + compression + value = compress(value, compression) + + with open(os.path.join(root, filename), "w") as handle: + handle.write(value) + + filenames.append(filename) + + final_files[key] = filenames + + if 'barcodes' in self._files: + with open(os.path.join(root, 'barcodes.txt'), 'w') as handle: + handle.writelines(self._files['barcodes']) + + if 'adapters' in self._files: + with open(os.path.join(root, 'adapters.txt'), 'w') as handle: + handle.writelines(self._files['adapters']) + + return final_files["input_1"], final_files["input_2"] + + def _do_call(self, root, input_1, input_2, compression, interleaved): + command = self._build_command(root, input_1, input_2, + compression, interleaved) + + with open(os.devnull, "w") as dev_null: + proc = subprocess.Popen(command, + stdin=dev_null, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + close_fds=True, + preexec_fn=os.setsid, + cwd=root) + + stdout, stderr = proc.communicate() + if stdout: + raise TestError("Unexpected output to STDOUT: %r" % (stdout,)) + + for value in self._info["stderr"]: + if re.search(value, stderr) is None: + raise TestError("Expected value not found in output:\n" + " Searching for:\n%s\n STDERR:\n%s" + % (pretty_output(value, 4), + pretty_output(stderr, 4, 5))) + + if proc.returncode != self._info["return_code"]: + raise TestError("ERROR: Expected return-code %i, but " + "AdapterRemoval returned %i:\n%s" + % (self._info["return_code"], + proc.returncode, + pretty_output(stderr, 2, 5))) + + def _check_file_creation(self, root, input_1, input_2, compression): + expected_files = set(self._files["output"]) + for key in ('barcodes', 'adapters'): + if key in self._files: + expected_files.add(key + '.txt') + + if compression != UNCOMPRESSED: + expected_files_ = set() + for value in expected_files: + if not (value.endswith(".settings") or value.endswith(".txt")): + expected_files_.add(value + "." + compression) + else: + expected_files_.add(value) + expected_files = expected_files_ + + observed_files = frozenset(os.listdir(root)) \ + - frozenset(input_1) - frozenset(input_2) + + if expected_files - observed_files: + raise TestError("ERROR: Expected output file(s) not created:\n" + " Expected: %r\n Observed: %r" + % (sorted(expected_files), sorted(observed_files))) + elif observed_files - expected_files: + raise TestError("ERROR: Unexpected output file(s) created: %r" + % (sorted(observed_files - expected_files))) + + def _check_file_contents(self, root, compression): + for filename, exp_data in sorted(self._files["output"].iteritems()): + obs_filename = os.path.join(root, filename) + if compression != UNCOMPRESSED: + if not filename.endswith(".settings"): + obs_filename += "." + compression + + obs_data = decompress(obs_filename) + if filename.endswith(".settings"): + exp_data = self._mangle_settings(exp_data) + obs_data = self._mangle_settings(obs_data) + + self._diff_file_pair_contents(os.path.join(self.root, filename), + os.path.join(root, filename), + exp_data, obs_data) + + def _diff_file_pair_contents(self, exp_filename, obs_filename, exp_data, obs_data): + if exp_data != obs_data: + lines = "".join(difflib.unified_diff(exp_data, obs_data, + "expected", "observed")) + + raise TestError("ERROR: Output file(s) differ:\n" + " Expected: %r\n Observed: %r\n Diff:\n%s" + % (exp_filename, obs_filename, + pretty_output(lines, 4))) + + def _build_command(self, root, input_1, input_2, compression, interleaved): + command = [os.path.abspath(_EXEC)] + if interleaved: + command.append("--interleaved-input") + + if 'barcodes' in self._files: + command.extend(('--barcode-list', 'barcodes.txt')) + + if input_1 or input_2: + if compression == BZIP2: + command.append("--bzip2") + elif compression == GZIP: + command.append("--gzip") + + if input_1: + command.append('--file1') + command.extend(input_1) + if input_2: + command.append('--file2') + command.extend(input_2) + + command.extend(self._info['arguments']) + + return [field % {"ROOT": root} for field in command] + + def _is_properly_paired(self): + input_1 = self._files["input_1"] + input_2 = self._files["input_2"] + + return input_1 and len(input_1) == len(input_2) + + @classmethod + def _mangle_settings(cls, handle): + result = [] + for line in handle: + line = re.sub(r"RNG seed: [0-9]+", "RNG seed: Enabled", line) + line = re.sub(r"AdapterRemoval ver\. .*", + "AdapterRemoval ver. X.Y.Z", line) + # Removed keyword to allow automatic interleaved tests + line = re.sub(r" interleaved paired-end reads", + r" paired-end reads", + line) + + result.append(line) + + return result + + @classmethod + def _collect_files(cls, root): + result = { + "input_1": [], + "input_2": [], + "output": {}, + } + + def read_lines(root, filename): + return open(os.path.join(root, filename)).readlines() + + abs_root = os.path.abspath(root) + for filename in sorted(os.listdir(root)): + if filename.startswith("input_1"): + result["input_1"].append(os.path.join(abs_root, filename)) + elif filename.startswith("input_2"): + result["input_2"].append(os.path.join(abs_root, filename)) + elif filename == 'barcodes.txt': + result["barcodes"] = read_lines(root, filename) + elif filename == 'adapters.txt': + result["adapters"] = read_lines(root, filename) + elif filename not in ('info.json', 'README'): + result["output"][filename] = read_lines(root, filename) + + return result + + @classmethod + def _read_info(cls, filename): + with open(filename) as handle: + text = handle.read() + raw_info = json.loads(text) + + if not isinstance(raw_info, types.DictType): + raise TestError('\'info.json\' does not contain dictionary.') + elif set(raw_info) - set(_INFO_FIELDS): + raise TestError('\'info.json\' does contains unexpected fields; ' + 'expected keys %r, but found keys unknown keys %r.' + % (sorted(_INFO_FIELDS), + sorted(set(raw_info) - set(_INFO_FIELDS)))) + + info = {"arguments": [], + "return_code": 0, + "stderr": []} + info.update(raw_info) + + for key, expected_type in _INFO_FIELDS.items(): + if not isinstance(info[key], expected_type): + raise TestError('Type of %r in \'info.json\' is %s, not a %s.' + % (key, type(info[key]), expected_type)) + elif isinstance(info[key], types.ListType): + for value in info[key]: + if not isinstance(value, types.StringTypes): + raise TestError('Type of value in %r in \'info.json\' ' + 'is %s, not a string.' + % (key, type(value))) + + return info + + @classmethod + def collect(cls, root, path=()): + tests = [] + + for filename in sorted(os.listdir(root)): + filepath = os.path.join(root, filename) + + if os.path.isdir(filepath): + tests.extend(cls.collect(filepath, path + (filename,))) + elif filename == 'info.json': + try: + test = TestCase(root, path) + except StandardError, error: + print_err("ERROR: %s reading test %r: %s" + % (error.__class__.__name__, + ' :: '.join(path), error)) + continue + + tests.append(test) + + return tests + + +def parse_args(argv): + parser = argparse.ArgumentParser() + parser.add_argument('work_dir', + help="Directory in which to run test-cases.") + parser.add_argument('source_dir', + help="Directory containing test-cases.") + + return parser.parse_args(argv) + + +def main(argv): + args = parse_args(argv) + if not os.path.exists(_EXEC): + print_err("ERROR: Executable does not exist: %r" % (_EXEC,)) + return 1 + + print('Reading test-cases from %r' % (args.source_dir,)) + tests = TestCase.collect(args.source_dir) + + if not os.path.exists(args.work_dir): + os.makedirs(args.work_dir) + + args.work_dir = tempfile.mkdtemp(dir=args.work_dir) + print('Writing test-cases results to %r' % (args.work_dir,)) + + n_failures = 0 + print('\nRunning tests:') + for idx, test in enumerate(tests, start=1): + print(" %i of %i: %s " % (idx, len(tests), test.name), end='') + label = 'unknown' + + try: + for label in test.run(args.work_dir): + print_ok(".", end="") + sys.stdout.flush() + except TestError, error: + n_failures += 1 + message = "\n ".join(str(error).split("\n")) + print_err(" %s for %s:\n %s" % (error.__class__.__name__, + label, message)) + else: + print_ok(" [OK]") + + if n_failures: + print_err("\n%i of %i tests failed .." % (n_failures, len(tests))) + else: + print_ok("\nAll %i tests succeeded .." % (len(tests),)) + + return n_failures + + +if __name__ == '__main__': + sys.exit(main(sys.argv[1:])) diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4051235691 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/collapse/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,147 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4051235691 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 0 0 0 0 +51 0 0 0 0 0 +52 0 0 0 0 0 +53 0 0 0 0 0 +54 0 0 0 0 0 +55 0 0 0 0 0 +56 0 0 0 0 0 +57 0 0 0 0 0 +58 0 0 0 0 0 +59 0 0 0 0 0 +60 0 0 0 0 0 +61 0 0 0 0 0 +62 0 0 0 0 0 +63 0 0 0 0 0 +64 0 0 0 0 0 +65 0 0 0 0 0 +66 0 0 0 0 0 +67 0 0 0 0 0 +68 0 0 0 0 0 +69 0 0 0 0 0 +70 0 0 0 0 0 +71 0 0 0 0 0 +72 0 0 0 0 0 +73 0 0 0 0 0 +74 0 0 0 0 0 +75 0 0 0 0 0 +76 0 0 0 0 0 +77 0 0 0 0 0 +78 0 0 0 0 0 +79 0 0 0 0 0 +80 0 0 0 0 0 +81 0 0 0 0 0 +82 0 0 0 0 0 +83 0 0 0 0 0 +84 0 0 0 0 0 +85 0 0 0 0 0 +86 0 0 0 0 0 +87 0 0 0 0 0 +88 0 0 0 0 0 +89 0 0 0 0 0 +90 0 0 0 0 0 +91 0 0 0 0 0 +92 0 0 0 0 0 +93 0 0 0 0 0 +94 0 0 0 0 0 +95 0 0 0 0 0 +96 0 0 0 0 0 +97 0 0 0 0 0 +98 0 0 0 0 0 +99 0 0 0 0 0 +100 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/collapse/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "999"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 999 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/discarded/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/combined_output/retained/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/crlf_newlines/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/crlf_newlines/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/defaults/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/defaults/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "13"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/your_output.discarded adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/maxlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/maxlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1833120783 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 13 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "999"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/your_output.discarded adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/minlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1752967089 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 999 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 217798732 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 100 +Average length of retained reads: 100 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 0 0 0 +100 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/excl_ns/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAANNNNNN ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,139 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 87921694 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 94 +Average length of retained reads: 94 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimns/incl_ns/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAA ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:977775532 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,144 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1434085985 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 99 +Average length of retained reads: 99 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 0 0 0 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/default/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/default/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/info.json adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/info.json --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities", "--minquality", "31"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,112 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1585058107 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 31: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 67 +Average length of retained reads: 67 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.truncated adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/excl_adapter/trimqualities/minq31/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT ++ +JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/your_output.collapsed adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,97 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 566778642 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@MT_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/collapse_truncated/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 566778642 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 1 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,97 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1432823771 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 0 0 0 +50 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--collapse", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,96 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1432823771 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 1 +Number of retained reads: 1 +Number of retained nucleotides: 49 +Average length of retained reads: 49 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 0 0 0 0 +44 0 0 0 0 0 +45 0 0 0 0 0 +46 0 0 0 0 0 +47 0 0 0 0 0 +48 0 0 0 0 0 +49 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@MT_AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "999"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1529034138 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 999 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/discarded/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 1756794576 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/combined_output/retained/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/crlf_newlines/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/crlf_newlines/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/defaults/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/defaults/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--maxlength", "13"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/your_output.discarded adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/maxlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/maxlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2394757988 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 13 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "999"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/your_output.discarded adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/minlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2314668317 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 999 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/input_1a.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/input_1a.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/input_1b.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/input_1b.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,16 @@ +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD +@read_150_10/1 +TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT ++ +<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,145 @@ +AdapterRemoval ver. 2.2.0 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 35713051 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 10 +Number of unaligned reads: 8 +Number of well aligned reads: 2 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 10 +Number of reads with adapters[1]: 2 +Number of retained reads: 10 +Number of retained nucleotides: 984 +Average length of retained reads: 98.4 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 0 0 0 +51 0 0 0 +52 0 0 0 +53 0 0 0 +54 0 0 0 +55 0 0 0 +56 0 0 0 +57 0 0 0 +58 0 0 0 +59 0 0 0 +60 0 0 0 +61 0 0 0 +62 0 0 0 +63 0 0 0 +64 0 0 0 +65 0 0 0 +66 0 0 0 +67 0 0 0 +68 0 0 0 +69 0 0 0 +70 0 0 0 +71 0 0 0 +72 0 0 0 +73 0 0 0 +74 0 0 0 +75 0 0 0 +76 0 0 0 +77 0 0 0 +78 0 0 0 +79 0 0 0 +80 0 0 0 +81 0 0 0 +82 0 0 0 +83 0 0 0 +84 0 0 0 +85 1 0 1 +86 0 0 0 +87 0 0 0 +88 0 0 0 +89 0 0 0 +90 0 0 0 +91 0 0 0 +92 0 0 0 +93 0 0 0 +94 0 0 0 +95 0 0 0 +96 0 0 0 +97 0 0 0 +98 0 0 0 +99 1 0 1 +100 8 0 8 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/multiple_input/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/multiple_input/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,40 @@ +@read_150_1/1 +CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT ++ +HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF +@read_150_2/1 +GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA ++ +HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 +@read_150_3/1 +TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA ++ +HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF +@read_150_4/1 +CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACA ++ +HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHH +@read_150_5/1 +TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT ++ +HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> +@read_150_7/1 +TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT ++ +GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH +@read_150_8/1 +TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC ++ +HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD +@read_150_10/1 +TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT ++ +<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "1"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/one/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/one/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "3"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/three/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/three/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--threads", "2"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: NA +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/threads/two/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/threads/two/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2489899758 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/excl_ns/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCNNNNNNNNATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,89 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2566824554 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 44 +Average length of retained reads: 44 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimns/incl_ns/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGC ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFF diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,95 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2679028121 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 50 +Average length of retained reads: 50 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 0 0 0 +46 0 0 0 +47 0 0 0 +48 0 0 0 +49 0 0 0 +50 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/default/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/default/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/info.json adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/info.json --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimqualities", "--minquality", "36"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/input_1.fastq adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.settings adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 2816594278 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 36: Yes +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 45 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.truncated adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/incl_adapter/trimqualities/minq36/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/your_output.discarded adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/collapse/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,47 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4215296776 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 0 +Number of truncated collapsed pairs: 0 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 913821732 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/discarded/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +N ++ +! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--combined-output", "--minlength", "0"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 984265443 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 0 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/only_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/combined_output/retained/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/your_output.discarded adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/crlf_newlines/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4288002672 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": [], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/your_output.discarded adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/your_output.discarded --- adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/defaults/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 4288002672 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 1 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of retained reads: 0 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 0 1 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/info.json adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/info.json --- adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--minlength", "0"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/input_1.fastq adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data +AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ++ +JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/your_output.settings adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 120751608 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 0 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 0 +Average length of retained reads: 0 + + +[Length distribution] +Length Mate1 Discarded All +0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/your_output.truncated adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/only_adapter/minlength/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/only_adapter/minlength/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@CTTTGTSeq_1_14286_0/1 meta data + ++ + diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim3p", "5"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 5 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 45 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim3p", "5", "20"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 5 20 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 45 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/3p_both_set/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/3p_both_set/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "5"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 5 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 45 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "4", "--trim3p", "5"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,86 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 4 +Trimming 3p: 5 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 41 +Average length of retained reads: 41 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "4", "3", "--trim3p", "5", "7"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,86 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 4 3 +Trimming 3p: 5 7 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 41 +Average length of retained reads: 41 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_and_3p_both_set/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trim5p", "5", "20"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 667770639 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 5 20 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 1 +Number of retained reads: 1 +Number of retained nucleotides: 45 +Average length of retained reads: 45 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 +31 0 0 0 +32 0 0 0 +33 0 0 0 +34 0 0 0 +35 0 0 0 +36 0 0 0 +37 0 0 0 +38 0 0 0 +39 0 0 0 +40 0 0 0 +41 0 0 0 +42 0 0 0 +43 0 0 0 +44 0 0 0 +45 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/your_output.truncated adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/your_output.truncated --- adapterremoval-2.2.2/tests/regression/se/trimfixed/5p_both_set/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/5p_both_set/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 +ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +JIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trim5p", "7"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +TAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT ++ +JIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,90 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 566778642 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 7 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 43 +Average length of retained reads: 43 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 0 0 0 0 +42 0 0 0 0 0 +43 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/info.json adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/info.json --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--collapse", "--trim5p", "4", "--trim3p", "5"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/input_1.fastq adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/input_1.fastq --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@AAGGGCSeq_1_5180_50/1 meta data +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG ++ +IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.collapsed adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.collapsed --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.collapsed 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@M_AAGGGCSeq_1_5180_50/1 meta data +GACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA ++ +JJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.settings adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.settings --- adapterremoval-2.2.2/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/se/trimfixed/collapse_5p_and_3p/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,88 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 566778642 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 4 +Trimming 3p: 5 +Trimming Ns: No +Trimming Phred scores <= 2: No +Trimming using sliding windows: No +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: Yes +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 0 +Number of well aligned reads: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 0 +Number of reads with adapters[1]: 1 +Number of full-length collapsed pairs: 1 +Number of truncated collapsed pairs: 0 +Number of retained reads: 1 +Number of retained nucleotides: 41 +Average length of retained reads: 41 + + +[Length distribution] +Length Mate1 Collapsed CollapsedTruncated Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 0 0 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 0 0 0 +31 0 0 0 0 0 +32 0 0 0 0 0 +33 0 0 0 0 0 +34 0 0 0 0 0 +35 0 0 0 0 0 +36 0 0 0 0 0 +37 0 0 0 0 0 +38 0 0 0 0 0 +39 0 0 0 0 0 +40 0 0 0 0 0 +41 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/info.json adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/info.json --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimwindows", "4", "--minquality", "20"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/input_1.fastq adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/input_1.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT ++ +7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/input_2.fastq adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/input_2.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTA ++ +IGHHFEIIIGFC5675565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.discarded adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.discarded --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGG ++ +IGHHFEIIIGFC diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.settings adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.settings --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,76 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 20: Yes +Trimming using sliding windows: 4 +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 30 +Average length of retained reads: 30 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 1 1 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 0 0 0 +28 0 0 0 0 0 +29 0 0 0 0 0 +30 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/excl_n/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/excl_n/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +NNTCAACAATAGGGTTTACGACCTCGATGN ++ +IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/info.json adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/info.json --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/input_1.fastq adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/input_1.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT ++ +7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/input_2.fastq adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/input_2.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/input_2.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGGTTGTAGTA ++ +IGHHFEIIIGFC5675565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.discarded adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.discarded --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.discarded 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/2 data meta +GTCAGCGAAGGG ++ +IGHHFEIIIGFC diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.settings adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.settings --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,73 @@ +AdapterRemoval ver. 2.1.7 +Trimming of paired-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 981230521 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 20: Yes +Trimming using sliding windows: 4 +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 + + +[Trimming statistics] +Total number of read pairs: 1 +Number of unaligned read pairs: 0 +Number of well aligned read pairs: 1 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of discarded mate 2 reads: 1 +Number of singleton mate 2 reads: 0 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 27 +Average length of retained reads: 27 + + +[Length distribution] +Length Mate1 Mate2 Singleton Discarded All +0 0 0 0 0 0 +1 0 0 0 0 0 +2 0 0 0 0 0 +3 0 0 0 0 0 +4 0 0 0 0 0 +5 0 0 0 0 0 +6 0 0 0 0 0 +7 0 0 0 0 0 +8 0 0 0 0 0 +9 0 0 0 0 0 +10 0 0 0 0 0 +11 0 0 0 0 0 +12 0 0 0 1 1 +13 0 0 0 0 0 +14 0 0 0 0 0 +15 0 0 0 0 0 +16 0 0 0 0 0 +17 0 0 0 0 0 +18 0 0 0 0 0 +19 0 0 0 0 0 +20 0 0 0 0 0 +21 0 0 0 0 0 +22 0 0 0 0 0 +23 0 0 0 0 0 +24 0 0 0 0 0 +25 0 0 0 0 0 +26 0 0 0 0 0 +27 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.singleton.truncated adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.singleton.truncated --- adapterremoval-2.2.2/tests/regression/trimwindows/pe/incl_n/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/pe/incl_n/your_output.singleton.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCAACAATAGGGTTTACGACCTCGATG ++ +IIIJJGJHGJJJGHJJJFGIIIGFC?: diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/info.json adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/info.json --- adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimwindows", "4", "--minquality", "20"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/input_1.fastq adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/input_1.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT ++ +7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/your_output.settings adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/your_output.settings --- adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,75 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: No +Trimming Phred scores <= 20: Yes +Trimming using sliding windows: 4 +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 30 +Average length of retained reads: 30 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/your_output.truncated adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/your_output.truncated --- adapterremoval-2.2.2/tests/regression/trimwindows/se/excl_n/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/excl_n/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +NNTCAACAATAGGGTTTACGACCTCGATGN ++ +IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/info.json adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/info.json --- adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/info.json 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/info.json 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,6 @@ +{ + "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], + "return_code": 0, + "stderr": [ + ] +} diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/input_1.fastq adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/input_1.fastq --- adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/input_1.fastq 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT ++ +7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/your_output.settings adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/your_output.settings --- adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/your_output.settings 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,72 @@ +AdapterRemoval ver. 2.1.7 +Trimming of single-end reads + + +[Adapter sequences] +Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG +Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT + + +[Adapter trimming] +RNG seed: 3702281079 +Alignment shift value: 2 +Global mismatch threshold: 0.333333 +Quality format (input): Phred+33 +Quality score max (input): 41 +Quality format (output): Phred+33 +Quality score max (output): 41 +Mate-number separator (input): '/' +Trimming 5p: 0 +Trimming 3p: 0 +Trimming Ns: Yes +Trimming Phred scores <= 20: Yes +Trimming using sliding windows: 4 +Minimum genomic length: 15 +Maximum genomic length: 4294967295 +Collapse overlapping reads: No +Minimum overlap (in case of collapse): 11 +Minimum adapter overlap: 0 + + +[Trimming statistics] +Total number of reads: 1 +Number of unaligned reads: 1 +Number of well aligned reads: 0 +Number of discarded mate 1 reads: 0 +Number of singleton mate 1 reads: 1 +Number of reads with adapters[1]: 0 +Number of retained reads: 1 +Number of retained nucleotides: 27 +Average length of retained reads: 27 + + +[Length distribution] +Length Mate1 Discarded All +0 0 0 0 +1 0 0 0 +2 0 0 0 +3 0 0 0 +4 0 0 0 +5 0 0 0 +6 0 0 0 +7 0 0 0 +8 0 0 0 +9 0 0 0 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 1 0 1 diff -Nru adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/your_output.truncated adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/your_output.truncated --- adapterremoval-2.2.2/tests/regression/trimwindows/se/incl_n/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/regression/trimwindows/se/incl_n/your_output.truncated 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,4 @@ +@ATAGCCSeq_1_2959_500/1 meta data +TCAACAATAGGGTTTACGACCTCGATG ++ +IIIJJGJHGJJJGHJJJFGIIIGFC?: diff -Nru adapterremoval-2.2.2/tests/strutils_test.cpp adapterremoval-2.2.3/tests/strutils_test.cpp --- adapterremoval-2.2.2/tests/strutils_test.cpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/strutils_test.cpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,170 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#include -#include -#include - -#include "strutils.hpp" - -namespace ar -{ - -/////////////////////////////////////////////////////////////////////////////// -// Tests for 'toupper' - -TEST(strutils_toupper, empty_input_empty_output) -{ - ASSERT_EQ("", toupper("")); -} - - -TEST(strutils_toupper, mixed_input) -{ - ASSERT_EQ("A1{2BZ`ZADEK", toupper("a1{2BZ`zAdeK")); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Tests for 'indent_lines' - -TEST(strutils_indent, empty_input_empty_output) -{ - ASSERT_EQ("", indent_lines("")); -} - - -TEST(strutils_indent, empty_line) -{ - ASSERT_EQ("\n", indent_lines("\n")); -} - - -TEST(strutils_indent, two_empty_lines) -{ - ASSERT_EQ("\n\n", indent_lines("\n\n")); -} - - -TEST(strutils_indent, three_empty_lines) -{ - ASSERT_EQ("\n\n\n", indent_lines("\n\n\n")); -} - - -TEST(strutils_indent, single_line_no_trailing_endline) -{ - ASSERT_EQ(" this is a test", indent_lines("this is a test")); -} - - -TEST(strutils_indent, single_line_trailing_endline) -{ - ASSERT_EQ(" this is a test\n", indent_lines("this is a test\n")); -} - - -TEST(strutils_indent, two_lines_no_trailing_endline) -{ - ASSERT_EQ(" this is a test\n line #2", - indent_lines("this is a test\nline #2")); -} - - -TEST(strutils_indent, two_lines_trailing_endline) -{ - ASSERT_EQ(" this is a test\n line #2\n", - indent_lines("this is a test\nline #2\n")); -} - - -TEST(strutils_indent, empty_line_middle) -{ - ASSERT_EQ(" this is a test\n\n line #2\n", - indent_lines("this is a test\n\nline #2\n")); -} - - -TEST(strutils_indent, empty_line_trailing) -{ - ASSERT_EQ(" this is a test\n line #2\n\n", - indent_lines("this is a test\nline #2\n\n")); -} - - -TEST(strutils_indent, empty_lines_trailing) -{ - ASSERT_EQ(" this is a test\n line #2\n\n\n", - indent_lines("this is a test\nline #2\n\n\n")); -} - - -/////////////////////////////////////////////////////////////////////////////// -// Tests for 'columnize_text' - -TEST(strutils_columnize, empty_lines) -{ - ASSERT_EQ("", columnize_text("")); - ASSERT_EQ("", columnize_text("\n")); - ASSERT_EQ("", columnize_text("\n\n")); - ASSERT_EQ("", columnize_text("\n\n\n")); -} - - -TEST(strutils_columnize, text_within_empty_lines) -{ - ASSERT_EQ("foo bar", columnize_text("foo bar")); - ASSERT_EQ("foo bar", columnize_text("foo\nbar")); - ASSERT_EQ("foo bar", columnize_text("foo\nbar\n")); - ASSERT_EQ("foo bar", columnize_text("\nfoo\nbar")); - ASSERT_EQ("foo bar", columnize_text("foo\nbar\n\n")); - ASSERT_EQ("foo bar", columnize_text("\nfoo\nbar\n")); - ASSERT_EQ("foo bar", columnize_text("\n\nfoo\nbar\n")); -} - - -TEST(strutils_columnize, maximum_width) -{ - ASSERT_EQ("foo bar zood", columnize_text("foo bar\nzood", 12)); - ASSERT_EQ("foo bar\nzood", columnize_text("foo bar\nzood", 11)); - ASSERT_EQ("foo bar\nzood", columnize_text("foo bar\nzood", 7)); - ASSERT_EQ("foo\nbar\nzood", columnize_text("foo bar\nzood", 6)); - ASSERT_EQ("foo\nbar\nzood", columnize_text("foo bar\nzood", 3)); - ASSERT_EQ("foo\nbar\nzood", columnize_text("foo bar\nzood", 1)); - ASSERT_EQ("foo\nbar\nzood", columnize_text("foo bar\nzood", 0)); -} - - -TEST(strutils_columnize, ljust) -{ - ASSERT_EQ("foo bar zood", columnize_text("foo bar\nzood", 12, 2)); - ASSERT_EQ("foo bar\n zood", columnize_text("foo bar\nzood", 11, 2)); - ASSERT_EQ("foo bar\n zood", columnize_text("foo bar\nzood", 7, 2)); - ASSERT_EQ("foo\n bar\n zood", columnize_text("foo bar\nzood", 6, 2)); - ASSERT_EQ("foo\n bar\n zood", columnize_text("foo bar\nzood", 3, 2)); - ASSERT_EQ("foo\n bar\n zood", columnize_text("foo bar\nzood", 1, 2)); - ASSERT_EQ("foo\n bar\n zood", columnize_text("foo bar\nzood", 0, 2)); -} - -} // namespace ar diff -Nru adapterremoval-2.2.2/tests/testing.hpp adapterremoval-2.2.3/tests/testing.hpp --- adapterremoval-2.2.2/tests/testing.hpp 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/tests/testing.hpp 1970-01-01 00:00:00.000000000 +0000 @@ -1,42 +0,0 @@ -/*************************************************************************\ - * AdapterRemoval - cleaning next-generation sequencing reads * - * * - * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * - * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * - * * - * If you use the program, please cite the paper: * - * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * - * Sequencing Reads, BMC Research Notes, 5:337 * - * http://www.biomedcentral.com/1756-0500/5/337/ * - * * - * This program is free software: you can redistribute it and/or modify * - * it under the terms of the GNU General Public License as published by * - * the Free Software Foundation, either version 3 of the License, or * - * (at your option) any later version. * - * * - * This program is distributed in the hope that it will be useful, * - * but WITHOUT ANY WARRANTY; without even the implied warranty of * - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * - * GNU General Public License for more details. * - * * - * You should have received a copy of the GNU General Public License * - * along with this program. If not, see . * -\*************************************************************************/ -#ifndef TESTING_H -#define TESTING_H - -#include - -#include "fastq.hpp" - - -namespace ar { - inline void PrintTo(const fastq& record, std::ostream* stream) - { - *stream << "'@" << record.header() << "\\n" - << record.sequence() << "\\n+\\n" - << record.qualities() << "\\n'"; - } -} - -#endif \ No newline at end of file diff -Nru adapterremoval-2.2.2/tests/unit/alignment_test.cpp adapterremoval-2.2.3/tests/unit/alignment_test.cpp --- adapterremoval-2.2.2/tests/unit/alignment_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/alignment_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,1201 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#include +#include +#include + +#include "testing.hpp" +#include "alignment.hpp" +#include "fastq.hpp" + + +#define TEST_ALIGNMENT_SETTER(TYPE, NAME) \ + ALN& NAME(TYPE value) \ + { \ + info.adapter_id = 0; \ + info.NAME = value; \ + return *this; \ + } + + +namespace ar +{ + + +bool operator==(const alignment_info& first, const alignment_info& second) +{ + return (first.offset == second.offset) + && (first.score == second.score) + && (first.length == second.length) + && (first.n_mismatches == second.n_mismatches) + && (first.n_ambiguous == second.n_ambiguous) + && (first.adapter_id == second.adapter_id); +} + + +struct ALN +{ + ALN() : info() {} + + TEST_ALIGNMENT_SETTER(int, score); + TEST_ALIGNMENT_SETTER(int, offset); + TEST_ALIGNMENT_SETTER(size_t, length); + TEST_ALIGNMENT_SETTER(size_t, n_mismatches); + TEST_ALIGNMENT_SETTER(size_t, n_ambiguous); + TEST_ALIGNMENT_SETTER(int, adapter_id); + + operator alignment_info() { + return info; + } + + alignment_info info; +}; + + +std::ostream& operator<<(std::ostream& stream, const alignment_info& aln) +{ + std::vector labels = { + "score", "offset", "length", + "n_mismatches", "n_ambiguous", + "adapter_id" + }; + + std::vector values = { + static_cast(aln.score), + static_cast(aln.offset), + static_cast(aln.length), + static_cast(aln.n_mismatches), + static_cast(aln.n_ambiguous), + static_cast(aln.adapter_id), + }; + + stream << "alignment_info("; + + bool any_streamed = false; + for (size_t i = 0; i < labels.size(); ++i) { + if (values.at(i)) { + if (any_streamed) { + stream << "\n "; + } + + stream << labels.at(i) << " = " << values.at(i); + any_streamed = true; + } + } + + return stream << ")"; +} + + +void REQUIRE_TRUNCATED_PE_IS_UNCHANGED(const alignment_info& alignment, + const fastq& record1, + const fastq& record2) +{ + fastq tmp_record1 = record1; + fastq tmp_record2 = record2; + REQUIRE(truncate_paired_ended_sequences(alignment, tmp_record1, tmp_record2) == 0); + REQUIRE(tmp_record1 == record1); + REQUIRE(tmp_record2 == record2); +} + + +fastq_pair_vec create_adapter_vec(const fastq& pcr1, const fastq& pcr2 = fastq()) +{ + fastq_pair_vec adapters; + adapters.push_back(fastq_pair(pcr1, pcr2)); + return adapters; +} + + +std::random_device g_seed; +std::mt19937 g_rng_instance(g_seed()); +std::mt19937* g_rng(&g_rng_instance); + + +/////////////////////////////////////////////////////////////////////////////// +// Cases for SE alignments (a = read 1, b = adapter, o = overlap): +// 1. No overlap = aaaaaa bbbbbb +// 2. Partial overlap = aaaaaooobbbbbb +// 3. Complete overlap = ooooooooo +// 4. a contains b = aaaaoooooo +// 5. b contains a = ooooobbbbb +// 6. a extends past b = aaaaoooooaaaa +// 7. b extends past a = bbbbooooobbbb +// 8. both extends past other = bbbbooooaaaa + + +/////////////////////////////////////////////////////////////////////////////// +// Case 1: No overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBBBBBB +// Expected result = suboptimal alignment or no overlap + +TEST_CASE("SE: Unalignable sequence yields default alignment", "[alignment::single_end]") +{ + const fastq record("Rec", "AAAA", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TTTT", "!!!!")); + + REQUIRE(align_single_ended_sequence(record, adapters, 0) == ALN()); +} + + +TEST_CASE("SE: Random sequences yields suboptimal alignment", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "TGAGACGGT", "!!!!!!!!!")); + + REQUIRE(align_single_ended_sequence(record, adapters, 0) == ALN().offset(6) + .length(2) + .n_mismatches(1)); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Case 2: Partial overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBBBBBB +// Expected result = optimal alignment between ends +TEST_CASE("SE: Partial alignment between ends", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTAA", "123457890"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGTAAGGT", "!!!!!!!!")); + const alignment_info expected = ALN().score(5).offset(4).length(5); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); +} + + +TEST_CASE("SE: Partial alignment with mismatches between ends", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTAA", "123457890"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGGAAGGT", "!!!!!!!!")); + const alignment_info expected = ALN().score(3).offset(4).length(5).n_mismatches(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); +} + + +TEST_CASE("SE: Partial alignment with ambiguous between ends", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTAA", "123457890"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "AGNAAGGT", "!!!!!!!!")); + const alignment_info expected = ALN().score(4).offset(4).length(5).n_ambiguous(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACGT", "1234")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Case 3: Complete overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBB +// Expected result = Optimal alignment involving all bases + +TEST_CASE("SE: Completely overlapping sequences", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(record); + const alignment_info expected = ALN().score(8).length(8); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +TEST_CASE("SE: Completely overlapping sequences with mismatches", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Rec", "GCGTAGTA", "!!!!!!!!")); + const alignment_info expected = ALN().score(6).length(8).n_mismatches(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +TEST_CASE("SE: Completely overlapping sequences with mismatches and ambiguous", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq_pair_vec adapter = create_adapter_vec(fastq("Rec", "GCGTAGTN", "!!!!!!!!")); + const alignment_info expected = ALN().score(5).length(8).n_mismatches(1).n_ambiguous(1); + const alignment_info result = align_single_ended_sequence(record, adapter, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Cases 4 and 5: Sequence A completely contains sequence B (and vice versa) +// AAAAAAAAAAA AAAA +// BBBBB BBBBBBBBBB +// Expected result = Optimal alignment involving all bases of the shortest read + +TEST_CASE("Complete adapter inside sequence", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGTA", "!!!!!")); + const alignment_info expected = ALN().score(5).offset(3).length(5); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); +} + + +TEST_CASE("Complete adapter inside sequence with mismatch", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TATTA", "!!!!!")); + const alignment_info expected = ALN().score(3).offset(3).length(5).n_mismatches(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); +} + + +TEST_CASE("Complete adapter inside sequence with ambiguous", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTA", "ABCDEFGH"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TAGNA", "!!!!!")); + const alignment_info expected = ALN().score(4).offset(3).length(5).n_ambiguous(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACG", "ABC")); +} + + +TEST_CASE("Complete sequence inside adapter", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGT", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTA", "!!!!!!!!")); + const alignment_info expected = ALN().score(4).length(4); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +TEST_CASE("Complete sequence inside adapter with mismatches", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGT", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "GCGTAGTA", "!!!!!!!!")); + const alignment_info expected = ALN().score(2).length(4).n_mismatches(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +TEST_CASE("Complete sequence inside adapter with ambiguous", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGT", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGNAGTA", "!!!!!!!!")); + const alignment_info expected = ALN().score(3).length(4).n_ambiguous(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Cases 6 and 7: Sequence A extends past sequence B (and vice versa) +// AAAAAAAAAAAAAA AAAA +// BBBBB BBBBBBBBBBBBB + +TEST_CASE("Sequence extends past adapter", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTATA", "0123456789"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "AGTA", "!!!!")); + const alignment_info expected = ALN().score(4).offset(4).length(4); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "ACGT", "0123")); +} + + +TEST_CASE("Sequence extends past adapter, no shift", "[alignment::single_end]") +{ + const fastq record("Rec", "CGTA", "#!%%"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); + const alignment_info expected = ALN().score(1).offset(3).length(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "CGT", "#!%")); +} + + +TEST_CASE("Sequence extends past adapter, shift 1", "[alignment::single_end]") +{ + const fastq record("Rec", "CGTA", "#!%%"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "ACGTAGTATA", "!!!!!!!!!!")); + const alignment_info expected = ALN().score(4).offset(-1).length(4); + const alignment_info result = align_single_ended_sequence(record, adapters, 1); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Cases 8: Both sequences extends past the other +// AAAAAAAAAAAAAAAAAA +// BBBBBBBBBBBBBBBBBB +// Expected result = Optimal alignment involving all overlapping bases + +TEST_CASE("Sequence and adapter extends past each other", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); + const alignment_info expected = ALN().score(10).offset(-4).length(10); + const alignment_info result = align_single_ended_sequence(record, adapters, 4); + REQUIRE(result == expected); + + fastq tmp_record = record; + truncate_single_ended_sequence(result, tmp_record); + REQUIRE(tmp_record == fastq("Rec", "", "")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Empty sequence or adapter + +TEST_CASE("Empty sequence alignment", "[alignment::single_end]") +{ + const fastq record; + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "CCGAACGTAGTATA", "!!!!!!!!!!!!!!")); + const alignment_info expected; + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); +} + + +TEST_CASE("Empty adapter alignment", "[alignment::single_end]") +{ + const fastq record("Rec", "ACGTAGTATATAGT", "!!!!!!!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq()); + const alignment_info expected; + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); +} + +/////////////////////////////////////////////////////////////////////////////// +// Misc + +TEST_CASE("Lower than possible shift is allowed", "[alignment::single_end]") +{ + const fastq record("Rec", "AAAA", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("Adp", "TTTT", "!!!!")); + const alignment_info expected; + const alignment_info result = align_single_ended_sequence(record, adapters, -10); + REQUIRE(result == expected); +} + + +TEST_CASE("Only adapter 1 is used", "[alignment::single_end]") +{ + const fastq_pair_vec adapters = create_adapter_vec(fastq("barcode", "AAA", "JJJ"), + fastq("barcode", "TTTAAA", "JJJJJJ")); + const fastq record("Rec", "CCCCTTTAAA", "0987654321"); + const alignment_info expected = ALN().score(3).offset(7).length(3); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); +} + + +TEST_CASE("Best matching adapter is returned: First", "[alignment::single_end]") +{ + fastq_pair_vec adapters; + adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); + adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); + + const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); + const alignment_info expected = ALN().score(6).offset(9).length(6); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); +} + + +TEST_CASE("Best matching adapter returned: Second", "[alignment::single_end]") +{ + fastq_pair_vec adapters; + adapters.push_back(fastq_pair(fastq("adapter", "TGCTGA", "JJJJJJ"), fastq())); + adapters.push_back(fastq_pair(fastq("adapter", "TGCTGC", "JJJJJJ"), fastq())); + + const fastq record("Read", "TAGTCGCTATGCTGC", "!!!!!!!!!103459"); + const alignment_info expected = ALN().score(6).offset(9).length(6).adapter_id(1); + const alignment_info result = align_single_ended_sequence(record, adapters, 0); + REQUIRE(result == expected); +} + + +TEST_CASE("Best matching adapter returned: Neither", "[alignment::single_end]") +{ + fastq_pair_vec barcodes; + barcodes.push_back(fastq_pair(fastq("barcode", "AAAAAA", "JJJJJJ"), fastq())); + barcodes.push_back(fastq_pair(fastq("barcode", "CCCCCC", "JJJJJJ"), fastq())); + + const fastq record = fastq("Read", "AACTGTACGTAGTT", "!!!!!!10345923"); + const alignment_info result = align_single_ended_sequence(record, barcodes, 0); + REQUIRE(result == ALN()); +} + + + +/////////////////////////////////////////////////////////////////////////////// +// Case 1 PE: No overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBBBBBB +// Expected result = suboptimal alignment or no overlap + +TEST_CASE("Unalignable sequence pair", "[alignment::paired_end]") +{ + const fastq record1("Rec", "AAAA", "!!!!"); + const fastq record2("Rec", "TTTT", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected; + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +TEST_CASE("No overlap in sequence pair", "[alignment::paired_end]") +{ + const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq record2("Rec", "TGAGACGGT", "!!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().offset(6).length(2).n_mismatches(1); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Case 2 PE: Partial overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBBBBBB +// Expected result = optimal alignment between ends + +TEST_CASE("Partial overlap in sequence pair", "[alignment::paired_end]") +{ + const fastq record1("Rec", "ACGTAGTAA", "!!!!!!!!!"); + const fastq record2("Rec", "AGTAAGGT", "!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(5).offset(4).length(5); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Case 3 PE: Complete overlap between sequences: +// AAAAAAAAAAA +// BBBBBBBBBBB +// Expected result = Optimal alignment involving all bases + +TEST_CASE("Completely overlapping sequence pair", "[alignment::paired_end]") +{ + const fastq record1("Rec", "ACGTAGTA", "!!!!!!!!"); + const fastq record2 = record1; + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(8).length(8); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Cases 4 and 5 PE: Sequence A completely contains sequence B (and vice versa) +// AAAAAAAAAAA AAAA +// BBBBB BBBBBBBBBB +// Expected result = Optimal alignment involving all bases of the shortest read + +TEST_CASE("Sequence A contains sequence B", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "ACGTAGTA", "!!!!!!!!"); + const fastq record2("Rec2", "TAGTA", "!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(5).offset(3).length(5); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +TEST_CASE("Sequence B contains sequence A", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "ACGT", "!!!!"); + const fastq record2("Rec2", "ACGTAGTA", "!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(4).length(4); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + REQUIRE_TRUNCATED_PE_IS_UNCHANGED(result, record1, record2); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Cases 6 and 7 PE: Sequence A extends past sequence B (and vice versa) +// AAAAAAAAAAAAAA AAAA +// BBBBB BBBBBBBBBBBBB +TEST_CASE("Sequence A extends past sequence B", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "ACGTAGTACG", "!!!!!!!!!!"); + const fastq record2("Rec2", "AGTA", "!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(6).offset(4).length(6); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record1 = record1; + fastq tmp_record2 = record2; + REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 1); + REQUIRE(tmp_record1 == fastq("Rec1", "ACGTAGTA", "!!!!!!!!")); + REQUIRE(tmp_record2 == fastq("Rec2", "AGTA", "!!!!")); +} + + +TEST_CASE("Sequence B extends past sequence A", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "CGTA", "!!!!"); + const fastq record2("Rec2", "ACCGTAGTAT", "!!!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(6).offset(-2).length(6); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record1 = record1; + fastq tmp_record2 = record2; + REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 1); + REQUIRE(tmp_record1 == fastq("Rec1", "CGTA", "!!!!")); + REQUIRE(tmp_record2 == fastq("Rec2", "CGTAGTAT", "!!!!!!!!")); +} + +/////////////////////////////////////////////////////////////////////////////// +// Cases 8 PE: Both sequences extends past the other +// AAAAAAAAAAAAAAAAAA +// BBBBBBBBBBBBBBBBBB +// Expected result = Optimal alignment involving all overlapping bases + +TEST_CASE("Sequences extends past each other", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "ACGTAGTATACGCT", "!!!!!!!!!!!!!!"); + const fastq record2("Rec2", "GTACACGTAGTATA", "!!!!!!!!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CGCTGA", "!!!!!!"), + fastq("PCR2", "TGTAC", "!!!!!")); + const alignment_info expected = ALN().score(18).offset(-4).length(18); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result == expected); + + fastq tmp_record1 = record1; + fastq tmp_record2 = record2; + REQUIRE(truncate_paired_ended_sequences(result, tmp_record1, tmp_record2) == 2); + REQUIRE(tmp_record1 == fastq("Rec1", "ACGTAGTATA", "!!!!!!!!!!")); + REQUIRE(tmp_record2 == fastq("Rec2", "ACGTAGTATA", "!!!!!!!!!!")); +} + + +TEST_CASE("Adapter only sequences", "[alignment::paired_end]") +{ + const fastq record1("Rec1", "CCCGAC", "!!!!!!"); + const fastq record2("Rec2", "ATGCCTT", "!!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), + fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); + const alignment_info expected = ALN().score(13).offset(-7).length(13); + const alignment_info result = align_paired_ended_sequences(record1, record2, adapters, 0); + + REQUIRE(result == expected); +} + + +TEST_CASE("Adapter only sequences, with missing base", "[alignment::paired_end]") +{ + // Test the case where both reads are adapters, but are missing a single base + // Normally, alignments that do not invovle read1 vs read2 are skipped, but + // missing bases may cause some alignments to be missed. + const fastq record1("Rec1", "CCGACC", "!!!!!!"); + const fastq record2("Rec2", "ATGCCT", "!!!!!!"); + const fastq_pair_vec adapters = create_adapter_vec(fastq("PCR1", "CCCGACCCGT", "!!!!!!!!!!"), + fastq("PCR2", "AAGATGCCTT", "!!!!!!!!!!")); + + // Sub-optimal alignment: + // aagatgccttCCGACC + // ATGCCTcccgacccgt + const alignment_info expected_1 = ALN().score(1).offset(-3).length(9).n_mismatches(4); + const alignment_info result_1 = align_paired_ended_sequences(record1, record2, adapters, 0); + REQUIRE(result_1 == expected_1); + // Optimal alignment, only possible with shift + // aagatgccttCCGACC + // ATGCCTcccgacccgt + const alignment_info expected_2 = ALN().score(11).offset(-7).length(13).n_mismatches(1); + const alignment_info result_2 = align_paired_ended_sequences(record1, record2, adapters, 1); + REQUIRE(result_2 == expected_2); +} + + +/////////////////////////////////////////////////////////////////////////////// +// + +TEST_CASE("Invalid alignment", "[alignment::paired_end]") +{ + fastq record1("Rec", "", ""); + fastq record2("Rec", "", ""); + const alignment_info alignment = ALN().offset(1); + + REQUIRE_THROWS_AS(truncate_paired_ended_sequences(alignment, record1, record2), std::invalid_argument); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Collapsing of reads + +TEST_CASE("Collapse partial overlap", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATATTATA", "01234567"); + fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(4); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "ATATTATAACGT", "01234567EFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Collapse complete overlap", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATATTATAA", "JJJJJJJJJ"); + fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); + const alignment_info alignment = ALN().offset(-1); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 2); + const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Collapse complete overlap for mate 1", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATATTATAG", "JJJJJJJJJ"); + fastq record2("Rec2", "ATATTATA", "JJJJJJJJ"); + const alignment_info alignment = ALN(); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); + const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Collapse complete overlap for mate 2", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATATTATA", "JJJJJJJJ"); + fastq record2("Rec2", "AATATTATA", "JJJJJJJJJ"); + const alignment_info alignment = ALN().offset(-1); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); + const fastq collapsed_expected = fastq("Rec1", "ATATTATA", "wwwwwwww", FASTQ_ENCODING_SAM); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Unequal sequence lengths, mate 1 shorter", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATA", "012"); + fastq record2("Rec2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(3); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "ATANNNNACGT", "012ABCDEFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Unequal sequence lengths, mate 1 shorter, mate 2 extends past", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATA", "012"); + fastq record2("Rec2", "AANNNNACGT", "90ABCDEFGH"); + const alignment_info alignment = ALN().offset(-2); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 1); + const fastq collapsed_expected = fastq("Rec1", "ATANACGT", "012DEFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Unequal sequence lengths, mate 2 shorter", "[alignment::collapse]") +{ + fastq record1("Rec1", "ATATTATA", "01234567"); + fastq record2("Rec2", "ACG", "EFG"); + const alignment_info alignment = ALN().offset(8); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "ATATTATAACG", "01234567EFG"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Ambiguous sites are filled from mate", "[alignment::collapse]") +{ + fastq record1("Rec1", "NNNNNNTATA", "0123456789"); + fastq record2("Rec2", "ACGTNNNNNN", "ABCDEFGHIJ"); + const alignment_info alignment; + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "ACGTNNTATA", "ABCD!!6789"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Identical nucleotides gets higher qualities", "[alignment::collapse]") +{ + fastq record1("Rec1", "GCATGATATA", "012345!0:A"); + fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); + const alignment_info alignment = ALN().offset(6); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345(FBcEFGHIJ", FASTQ_ENCODING_SAM); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Identical nucleotides gets higher qualities, no more than 41", "[alignment::collapse]") +{ + fastq record1("Rec1", "GCATGATATA", "0123456789"); + fastq record2("Rec2", "TATATACAAC", "ABCDEFGHIJ"); + const alignment_info alignment = ALN().offset(6); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "GCATGATATATACAAC", "012345Z\\^`EFGHIJ", FASTQ_ENCODING_SAM); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Higher quality nucleotide is selected", "[alignment::collapse]") +{ + fastq record1("Rec1", "GCATGAGCAT", "012345!0:A"); + fastq record2("Rec2", "TATATACAAC", "(3&?EFGHIJ"); + const alignment_info alignment = ALN().offset(6); + REQUIRE(truncate_paired_ended_sequences(alignment, record1, record2) == 0); + const fastq collapsed_expected = fastq("Rec1", "GCATGATAATTACAAC", "012345(%5%EFGHIJ"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Randomly select between different nucleotides with same quality #1", "[alignment::collapse]") +{ + const fastq record1("Rec1", "G", "1"); + const fastq record2("Rec2", "T", "1"); + const alignment_info alignment; + std::seed_seq seed{1}; + std::mt19937 rng(seed); + + const fastq collapsed_expected = fastq("Rec1", "G", "#"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, &rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Randomly select between different nucleotides with same quality #2", "[alignment::collapse]") +{ + const fastq record1("Rec1", "G", "1"); + const fastq record2("Rec2", "T", "1"); + const alignment_info alignment; + std::seed_seq seed{2}; + std::mt19937 rng(seed); + + const fastq collapsed_expected = fastq("Rec1", "T", "#"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, &rng); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Set conflicts to N/! if no RNG is provided", "[alignment::collapse]") +{ + const fastq record1("Rec1", "G", "1"); + const fastq record2("Rec2", "T", "1"); + const alignment_info alignment; + std::seed_seq seed{2}; + std::mt19937 rng(seed); + + const fastq collapsed_expected = fastq("Rec1", "N", "!"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, nullptr); + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Offsets past the end throws", "[alignment::collapse]") +{ + const fastq record1("Rec1", "G", "1"); + const fastq record2("Rec2", "T", "1"); + const alignment_info alignment = ALN().offset(2); + REQUIRE_THROWS_AS(collapse_paired_ended_sequences(alignment, record1, record2, g_rng), std::invalid_argument); +} + + +TEST_CASE("Mate numbering is removed", "[alignment::collapse]") +{ + const fastq record1("Read/1", "ATATTATA", "01234567"); + const fastq record2("Read/2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(4); + const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Mate numbering removed, meta from 1 kept", "[alignment::collapse]") +{ + const fastq record1("Read/1 Meta1", "ATATTATA", "01234567"); + const fastq record2("Read/2 Meta2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(4); + const fastq collapsed_expected = fastq("Read Meta1", "ATATTATAACGT", "01234567EFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Mate numbering removed, non-standard separator", "[alignment::collapse]") +{ + const fastq record1("Read:1", "ATATTATA", "01234567"); + const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(4); + const fastq collapsed_expected = fastq("Read", "ATATTATAACGT", "01234567EFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng, ':'); + + REQUIRE(collapsed_result == collapsed_expected); +} + + +TEST_CASE("Mate numbering removed, non-standard separator, not set", "[alignment::collapse]") +{ + const fastq record1("Read:1", "ATATTATA", "01234567"); + const fastq record2("Read:2", "NNNNACGT", "ABCDEFGH"); + const alignment_info alignment = ALN().offset(4); + const fastq collapsed_expected = fastq("Read:1", "ATATTATAACGT", "01234567EFGH"); + const fastq collapsed_result = collapse_paired_ended_sequences(alignment, record1, record2, g_rng); + + REQUIRE(collapsed_result == collapsed_expected); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Adapter extraction + +TEST_CASE("Extracting empty sequences yields empty sequences #1", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "", ""); + const fastq expected_2 = fastq("read2", "", ""); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == expected_1); + REQUIRE(read2 == expected_2); +} + + +TEST_CASE("Extracting empty sequences yields empty sequences #2", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "", ""); + const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = fastq("read2", "GGGGCC", "!!!!!!"); + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting empty sequences yields empty sequences #3", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "", ""); + fastq read1 = fastq("read1", "", ""); + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting empty sequences yields empty sequences #4", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "", ""); + const fastq expected_2 = fastq("read2", "", ""); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting with no alignment yields empty sequences", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting with partial overlap yields empty sequences", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN().offset(2), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting with complete overlap yields empty sequences", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting sequence 2 inside sequence 1 yields empty sequences", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "GGCC", "!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN().offset(2), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting sequence 1 inside sequence 2 yields empty sequences", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATT", "!!!!"); + const fastq expected_2 = fastq("read2", "GGGGCC", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting sequence 1 extending past sequence 2", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "AATTTTCC", "12345678"); + const fastq expected_2 = fastq("read2", "GGGGGG", "!!!!!!"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN(), read1, read2); + REQUIRE(read1 == fastq("read1", "CC", "78")); + REQUIRE(read2 == fastq("read2", "", "")); +} + + +TEST_CASE("Extracting sequence 2 extending past sequence 1", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "TTTTTT", "!!!!!!"); + const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN().offset(-2), read1, read2); + REQUIRE(read1 == fastq("read1", "", "")); + REQUIRE(read2 == fastq("read2", "AA", "12")); +} + + +TEST_CASE("Extracting both sequences extending past each other", "[alignment::extract_adapter_sequences]") +{ + const fastq expected_1 = fastq("read1", "TTTTTTCCC", "ABCDEFGHI"); + const fastq expected_2 = fastq("read2", "AAGGGGGG", "12345678"); + fastq read1 = expected_1; + fastq read2 = expected_2; + extract_adapter_sequences(ALN().offset(-2), read1, read2); + REQUIRE(read1 == fastq("read1", "CCC", "GHI")); + REQUIRE(read2 == fastq("read2", "AA", "12")); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Brute-force checking of alignment calculations +// Simply check all combinations involving 3 bases varying, for a range of +// sequence lengths to help catch corner cases with the optimizations + +// The function is not exposed, so a declaration is required +bool compare_subsequences(const alignment_info& best, alignment_info& current, + const char* seq_1_ptr, const char* seq_2_ptr); + + +/** Naive reimplementation of alignment calculation. **/ +void update_alignment(alignment_info& aln, + const std::string& a, + const std::string& b, + size_t nbases) +{ + // Don't count all these checks in test statistics + if (a.length() != b.length()) { + REQUIRE(a.length() == b.length()); + } + + for (size_t i = 0; i < nbases; ++i) { + const char nt1 = a.at(i); + const char nt2 = b.at(i); + + if (nt1 == 'N' || nt2 == 'N') { + aln.n_ambiguous++; + } else if (nt1 == nt2) { + aln.score++; + } else { + aln.n_mismatches++; + aln.score--; + } + } +} + + +/** Returns all 3 nt combinations of the bases ACGTN. **/ +std::vector get_combinations() +{ + std::vector result; + const std::string nts = "ACGTN"; + for (size_t i = 0; i < nts.length(); ++i) { + for (size_t j = 0; j < nts.length(); ++j) { + for (size_t k = 0; k < nts.length(); ++k) { + std::string combination(3, 'A'); + combination.at(0) = nts.at(i); + combination.at(1) = nts.at(j); + combination.at(2) = nts.at(k); + result.push_back(combination); + } + } + } + + return result; +} + + +TEST_CASE("Brute-force validation", "[alignment::compare_subsequences]") +{ + const alignment_info best; + const std::vector combinations = get_combinations(); + for (size_t seqlen = 10; seqlen <= 20; ++seqlen) { + for (size_t pos = 0; pos < seqlen; ++pos) { + const size_t nbases = std::min(3, seqlen - pos); + + for (size_t i = 0; i < combinations.size(); ++i) { + for (size_t j = 0; j < combinations.size(); ++j) { + alignment_info expected; + expected.length = seqlen; + expected.score = seqlen - nbases; + update_alignment(expected, combinations.at(i), combinations.at(j), nbases); + + std::string mate1 = std::string(seqlen, 'A'); + mate1.replace(pos, nbases, combinations.at(i).substr(0, nbases)); + std::string mate2 = std::string(seqlen, 'A'); + mate2.replace(pos, nbases, combinations.at(j).substr(0, nbases)); + + alignment_info current; + current.length = seqlen; + compare_subsequences(best, current, mate1.c_str(), mate2.c_str()); + + // Don't count all these checks in test statistics + if (!(current == expected)) { + REQUIRE(current == expected); + } + } + } + } + } +} + +} // namespace ar diff -Nru adapterremoval-2.2.2/tests/unit/argparse_test.cpp adapterremoval-2.2.3/tests/unit/argparse_test.cpp --- adapterremoval-2.2.2/tests/unit/argparse_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/argparse_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,511 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#include +#include +#include + +#include "testing.hpp" +#include "argparse.hpp" +#include "debug.hpp" + +namespace ar +{ + +typedef std::unique_ptr consumer_autoptr; + + +/////////////////////////////////////////////////////////////////////////////// +// flag -- boolean + +TEST_CASE("Flag defaults", "[argparse::flag]") +{ + consumer_autoptr ptr(new argparse::flag()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == " "); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == "off"); +} + + +TEST_CASE("Flag help", "[argparse::flag]") +{ + consumer_autoptr ptr(new argparse::flag(nullptr, "help! help!")); + REQUIRE(ptr->help() == "help! help!"); +} + + +TEST_CASE("Flag consumes no arguments", "[argparse::flag]") +{ + string_vec arguments; + arguments.push_back("--foo"); + consumer_autoptr ptr(new argparse::flag()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); + CHECK(ptr->is_set()); +} + + +TEST_CASE("Flag may be called on end of arguments", "[argparse::flag]") +{ + const string_vec arguments; + consumer_autoptr ptr(new argparse::flag()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); + CHECK(ptr->is_set()); +} + + +TEST_CASE("Flag uses sink with true", "[argparse::flag]") +{ + bool sink = true; + consumer_autoptr ptr(new argparse::flag(&sink)); + REQUIRE(ptr->to_str() == "on"); + const string_vec arguments; + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); + CHECK(ptr->is_set()); + CHECK(sink); + REQUIRE(ptr->to_str() == "on"); +} + + +TEST_CASE("Flag uses sink with false", "[argparse::flag]") +{ + bool sink = false; + consumer_autoptr ptr(new argparse::flag(&sink)); + REQUIRE(ptr->to_str() == "off"); + const string_vec arguments; + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); + CHECK(ptr->is_set()); + CHECK(sink); + REQUIRE(ptr->to_str() == "on"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// any -- string + +TEST_CASE("Any defaults", "[argparse::any]") +{ + consumer_autoptr ptr(new argparse::any()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == ""); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == ""); +} + + +TEST_CASE("Any value set", "[argparse::any]") +{ + std::string sink = "kitchensink"; + consumer_autoptr ptr(new argparse::any(&sink, "a metavar", "help!")); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == "a metavar"); + REQUIRE(ptr->help() == "help!"); + REQUIRE(ptr->to_str() == "kitchensink"); +} + + +TEST_CASE("Any consumes one argument", "[argparse::any]") +{ + string_vec arguments; + arguments.push_back("foo"); + arguments.push_back("bar"); + consumer_autoptr ptr(new argparse::any()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(ptr->to_str() == "foo"); +} + + +TEST_CASE("Any cannot consume empty list of arguments", "[argparse::any]") +{ + const string_vec arguments; + consumer_autoptr ptr(new argparse::any()); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->to_str() == ""); +} + + +TEST_CASE("Any with empty sink", "[argparse::any]") +{ + std::string sink; + consumer_autoptr ptr(new argparse::any(&sink)); + REQUIRE(ptr->to_str() == ""); + string_vec arguments; + arguments.push_back("foo"); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == "foo"); + REQUIRE(ptr->to_str() == "foo"); +} + + +TEST_CASE("Any with preset sink", "[argparse::any]") +{ + std::string sink = "kitchensink"; + consumer_autoptr ptr(new argparse::any(&sink)); + REQUIRE(ptr->to_str() == "kitchensink"); + string_vec arguments; + arguments.push_back("foo"); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == "foo"); + REQUIRE(ptr->to_str() == "foo"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// many -- strings + +TEST_CASE("Many defaults", "[argparse::many]") +{ + string_vec sink; + consumer_autoptr ptr(new argparse::many(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == ""); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == ""); +} + + +TEST_CASE("Many with defaults", "[argparse::many]") +{ + string_vec sink; + sink.push_back("kitchensink"); + + consumer_autoptr ptr(new argparse::many(&sink, "a metavar", "help!")); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == "a metavar"); + REQUIRE(ptr->help() == "help!"); + REQUIRE(ptr->to_str() == "kitchensink"); +} + + +TEST_CASE("Many consumes one argument", "[argparse::many]") +{ + string_vec arguments; + arguments.push_back("foo"); + + string_vec sink; + consumer_autoptr ptr(new argparse::many(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(ptr->to_str() == "foo"); +} + + +TEST_CASE("Many consumes two arguments", "[argparse::many]") +{ + string_vec arguments; + arguments.push_back("foo"); + arguments.push_back("bar"); + + string_vec sink; + consumer_autoptr ptr(new argparse::many(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 2); + CHECK(ptr->is_set()); + REQUIRE(ptr->to_str() == "foo;bar"); +} + + +TEST_CASE("Many consumes until next option", "[argparse::many]") +{ + string_vec arguments; + arguments.push_back("foo"); + arguments.push_back("--zoo"); + arguments.push_back("bar"); + + string_vec sink; + consumer_autoptr ptr(new argparse::many(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(ptr->to_str() == "foo"); +} + + +TEST_CASE("Many does not consume empty list of arguments", "[argparse::many]") +{ + string_vec sink; + const string_vec arguments; + consumer_autoptr ptr(new argparse::many(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 0); + CHECK(ptr->is_set()); + REQUIRE(ptr->to_str() == ""); +} + + +TEST_CASE("Many with empty sink", "[argparse::many]") +{ + string_vec sink; + string_vec expected; + expected.push_back("foo"); + + consumer_autoptr ptr(new argparse::many(&sink)); + REQUIRE(ptr->to_str() == ""); + string_vec arguments; + arguments.push_back("foo"); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == expected); + REQUIRE(ptr->to_str() == "foo"); +} + + +TEST_CASE("many with preset sink", "[argparse::many]") +{ + string_vec sink; + sink.push_back("kitchensink"); + string_vec expected; + expected.push_back("foo"); + + consumer_autoptr ptr(new argparse::many(&sink)); + REQUIRE(ptr->to_str() == "kitchensink"); + string_vec arguments; + arguments.push_back("foo"); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == expected); + REQUIRE(ptr->to_str() == "foo"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// knob -- unsigned + +TEST_CASE("Knob defaults", "[argparse::knob]") +{ + unsigned sink = 0; + consumer_autoptr ptr(new argparse::knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == ""); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == "0"); +} + + +TEST_CASE("Knob requires a sink", "[argparse::knob]") +{ + REQUIRE_THROWS_AS(argparse::knob(nullptr), assert_failed); +} + + +TEST_CASE("Knot values are set", "[argparse::knob]") +{ + unsigned sink = 7913; + consumer_autoptr ptr(new argparse::knob(&sink, "a metavar", "help!")); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == "a metavar"); + REQUIRE(ptr->help() == "help!"); + REQUIRE(ptr->to_str() == "7913"); +} + + +TEST_CASE("Knob consumes one argument", "[argparse::knob]") +{ + unsigned sink = 0; + string_vec arguments; + arguments.push_back("47"); + arguments.push_back("bar"); + consumer_autoptr ptr(new argparse::knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == 47); + REQUIRE(ptr->to_str() == "47"); +} + + +TEST_CASE("Knob does not consume empty list of arguments", "[argparse::knob]") +{ + unsigned sink = 13; + const string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); + CHECK(!ptr->is_set()); + REQUIRE(sink == 13); + REQUIRE(ptr->to_str() == "13"); +} + + +TEST_CASE("Knob rejects negative values", "[argparse::knob]") +{ + unsigned sink = 13; + string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + arguments.push_back("-47"); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); + CHECK(!ptr->is_set()); + REQUIRE(sink == 13); + REQUIRE(ptr->to_str() == "13"); +} + + +TEST_CASE("Knob accepts zero", "[argparse::knob]") +{ + unsigned sink = 13; + string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + arguments.push_back("0"); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == 0); + REQUIRE(ptr->to_str() == "0"); +} + + +TEST_CASE("Knob accepts unsigned upper bound", "[argparse::knob]") +{ + unsigned sink = 13; + string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + arguments.push_back("4294967295"); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == 4294967295); + REQUIRE(ptr->to_str() == "4294967295"); +} + + +TEST_CASE("Knob rejects past unsigned upper bound", "[argparse::knob]") +{ + unsigned sink = 13; + string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + arguments.push_back("4294967296"); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); + CHECK(!ptr->is_set()); +} + + +TEST_CASE("Knob rejects trailing garbage", "[argparse::knob]") +{ + unsigned sink = 13; + string_vec arguments; + consumer_autoptr ptr(new argparse::knob(&sink)); + arguments.push_back("7913w"); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); + CHECK(!ptr->is_set()); +} + + +/////////////////////////////////////////////////////////////////////////////// +// floaty_knob -- double + +TEST_CASE("Floaty knob defaults", "[argparse::floaty_knob]") +{ + double sink = 0; + consumer_autoptr ptr(new argparse::floaty_knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == ""); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == "0"); +} + + +TEST_CASE("Floaty knob treats NaN as unset", "[argparse::floaty_knob]") +{ + double sink = std::numeric_limits::quiet_NaN(); + consumer_autoptr ptr(new argparse::floaty_knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == ""); + REQUIRE(ptr->help() == ""); + REQUIRE(ptr->to_str() == ""); +} + + +TEST_CASE("Floaty knob requires sink", "[argparse::floaty_knob]") +{ + REQUIRE_THROWS_AS(argparse::floaty_knob(nullptr), assert_failed); +} + + +TEST_CASE("Floaty knob with values", "[argparse::floaty_knob]") +{ + double sink = 3.142; + consumer_autoptr ptr(new argparse::floaty_knob(&sink, "a metavar", "help!")); + CHECK(!ptr->is_set()); + REQUIRE(ptr->metavar() == "a metavar"); + REQUIRE(ptr->help() == "help!"); + REQUIRE(ptr->to_str() == "3.142"); +} + + +TEST_CASE("Floaty knob consumes one argument", "[argparse::floaty_knob]") +{ + double sink = 47.0; + string_vec arguments; + arguments.push_back("-19.84"); + arguments.push_back("bar"); + consumer_autoptr ptr(new argparse::floaty_knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == 1); + CHECK(ptr->is_set()); + REQUIRE(sink == -19.84); + REQUIRE(ptr->to_str() == "-19.84"); +} + + +TEST_CASE("Floaty knob does not consume empty list of arguments", "[argparse::floaty_knob]") +{ + double sink = 13; + const string_vec arguments; + consumer_autoptr ptr(new argparse::floaty_knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == static_cast(-1)); + CHECK(!ptr->is_set()); + REQUIRE(sink == 13); + REQUIRE(ptr->to_str() == "13"); +} + + +TEST_CASE("Floaty knob rejects trailing garbage", "[argparse::floaty_knob]") +{ + double sink = 47.0; + string_vec arguments; + arguments.push_back("-19.84wat"); + consumer_autoptr ptr(new argparse::floaty_knob(&sink)); + CHECK(!ptr->is_set()); + REQUIRE(ptr->consume(arguments.begin(), arguments.end()) == -1); + CHECK(!ptr->is_set()); +} + + +/////////////////////////////////////////////////////////////////////////////// +// parser + +} // namespace ar diff -Nru adapterremoval-2.2.2/tests/unit/catch.hpp adapterremoval-2.2.3/tests/unit/catch.hpp --- adapterremoval-2.2.2/tests/unit/catch.hpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/catch.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,11550 @@ +/* + * Catch v2.0.0-develop.2 + * Generated: 2017-08-18 15:57:31.231591 + * ---------------------------------------------------------- + * This file has been merged from multiple headers. Please don't edit it directly + * Copyright (c) 2017 Two Blue Cubes Ltd. All rights reserved. + * + * Distributed under the Boost Software License, Version 1.0. (See accompanying + * file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) + */ +#ifndef TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED +#define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED +// start catch.hpp + + +#ifdef __clang__ +# pragma clang system_header +#elif defined __GNUC__ +# pragma GCC system_header +#endif + +// start catch_suppress_warnings.h + +#ifdef __clang__ +# ifdef __ICC // icpc defines the __clang__ macro +# pragma warning(push) +# pragma warning(disable: 161 1682) +# else // __ICC +# pragma clang diagnostic ignored "-Wglobal-constructors" +# pragma clang diagnostic ignored "-Wvariadic-macros" +# pragma clang diagnostic ignored "-Wc99-extensions" +# pragma clang diagnostic ignored "-Wunused-variable" +# pragma clang diagnostic push +# pragma clang diagnostic ignored "-Wpadded" +# pragma clang diagnostic ignored "-Wswitch-enum" +# pragma clang diagnostic ignored "-Wcovered-switch-default" +# endif +#elif defined __GNUC__ +# pragma GCC diagnostic ignored "-Wvariadic-macros" +# pragma GCC diagnostic ignored "-Wunused-variable" +# pragma GCC diagnostic ignored "-Wparentheses" + +# pragma GCC diagnostic push +# pragma GCC diagnostic ignored "-Wpadded" +#endif +// end catch_suppress_warnings.h +#if defined(CATCH_CONFIG_MAIN) || defined(CATCH_CONFIG_RUNNER) +# define CATCH_IMPL +# define CATCH_CONFIG_EXTERNAL_INTERFACES +#endif + +#ifdef CATCH_IMPL +# ifndef CLARA_CONFIG_MAIN +# define CLARA_CONFIG_MAIN_NOT_DEFINED +# define CLARA_CONFIG_MAIN +# endif +#endif + +// start catch_context.h + +#include + +namespace Catch { + + class TestCase; + class Stream; + struct IResultCapture; + struct IRunner; + struct IConfig; + + using IConfigPtr = std::shared_ptr; + + struct IContext + { + virtual ~IContext(); + + virtual IResultCapture* getResultCapture() = 0; + virtual IRunner* getRunner() = 0; + virtual IConfigPtr getConfig() const = 0; + }; + + struct IMutableContext : IContext + { + virtual ~IMutableContext(); + virtual void setResultCapture( IResultCapture* resultCapture ) = 0; + virtual void setRunner( IRunner* runner ) = 0; + virtual void setConfig( IConfigPtr const& config ) = 0; + }; + + IContext& getCurrentContext(); + IMutableContext& getCurrentMutableContext(); + void cleanUpContext(); +} + +// end catch_context.h +// start catch_tag_alias_autoregistrar.h + +// start catch_common.h + +// start catch_compiler_capabilities.h + +// Detect a number of compiler features - by compiler +// The following features are defined: +// +// CATCH_CONFIG_COUNTER : is the __COUNTER__ macro supported? +// CATCH_CONFIG_WINDOWS_SEH : is Windows SEH supported? +// CATCH_CONFIG_POSIX_SIGNALS : are POSIX signals supported? +// **************** +// Note to maintainers: if new toggles are added please document them +// in configuration.md, too +// **************** + +// In general each macro has a _NO_ form +// (e.g. CATCH_CONFIG_NO_POSIX_SIGNALS) which disables the feature. +// Many features, at point of detection, define an _INTERNAL_ macro, so they +// can be combined, en-mass, with the _NO_ forms later. + +#ifdef __cplusplus + +# if __cplusplus >= 201402L +# define CATCH_CPP14_OR_GREATER +# endif + +#endif + +#ifdef __clang__ + +# define CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS \ + _Pragma( "clang diagnostic push" ) \ + _Pragma( "clang diagnostic ignored \"-Wexit-time-destructors\"" ) +# define CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS \ + _Pragma( "clang diagnostic pop" ) + +# define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS \ + _Pragma( "clang diagnostic push" ) \ + _Pragma( "clang diagnostic ignored \"-Wparentheses\"" ) +# define CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS \ + _Pragma( "clang diagnostic pop" ) + +#endif // __clang__ + +//////////////////////////////////////////////////////////////////////////////// +// We know some environments not to support full POSIX signals +#if defined(__CYGWIN__) || defined(__QNX__) + +# if !defined(CATCH_CONFIG_POSIX_SIGNALS) +# define CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS +# endif + +#endif + +#ifdef __OS400__ +# define CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS +# define CATCH_CONFIG_COLOUR_NONE +#endif + +//////////////////////////////////////////////////////////////////////////////// +// Cygwin +#ifdef __CYGWIN__ + +// Required for some versions of Cygwin to declare gettimeofday +// see: http://stackoverflow.com/questions/36901803/gettimeofday-not-declared-in-this-scope-cygwin +# define _BSD_SOURCE + +#endif // __CYGWIN__ + +//////////////////////////////////////////////////////////////////////////////// +// Borland +#ifdef __BORLANDC__ + +#endif // __BORLANDC__ + +//////////////////////////////////////////////////////////////////////////////// +// EDG +#ifdef __EDG_VERSION__ + +#endif // __EDG_VERSION__ + +//////////////////////////////////////////////////////////////////////////////// +// Digital Mars +#ifdef __DMC__ + +#endif // __DMC__ + +//////////////////////////////////////////////////////////////////////////////// +// GCC +#ifdef __GNUC__ + +#endif // __GNUC__ + +//////////////////////////////////////////////////////////////////////////////// +// Visual C++ +#ifdef _MSC_VER + +#define CATCH_INTERNAL_CONFIG_WINDOWS_SEH + +#endif // _MSC_VER + +//////////////////////////////////////////////////////////////////////////////// + +// Use __COUNTER__ if the compiler supports it +#if ( defined _MSC_VER && _MSC_VER >= 1300 ) || \ + ( defined __GNUC__ && ( __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3 )) ) || \ + ( defined __clang__ && __clang_major__ >= 3 ) + +#define CATCH_INTERNAL_CONFIG_COUNTER + +#endif + +// Now set the actual defines based on the above + anything the user has configured + +// Use of __COUNTER__ is suppressed if __JETBRAINS_IDE__ is #defined (meaning we're being parsed by a JetBrains IDE for +// analytics) because, at time of writing, __COUNTER__ is not properly handled by it. +// This does not affect compilation +#if defined(CATCH_INTERNAL_CONFIG_COUNTER) && !defined(CATCH_CONFIG_NO_COUNTER) && !defined(CATCH_CONFIG_COUNTER) && !defined(__JETBRAINS_IDE__) +# define CATCH_CONFIG_COUNTER +#endif +#if defined(CATCH_INTERNAL_CONFIG_WINDOWS_SEH) && !defined(CATCH_CONFIG_NO_WINDOWS_SEH) && !defined(CATCH_CONFIG_WINDOWS_SEH) +# define CATCH_CONFIG_WINDOWS_SEH +#endif +// This is set by default, because we assume that unix compilers are posix-signal-compatible by default. +#if !defined(CATCH_INTERNAL_CONFIG_NO_POSIX_SIGNALS) && !defined(CATCH_CONFIG_NO_POSIX_SIGNALS) && !defined(CATCH_CONFIG_POSIX_SIGNALS) +# define CATCH_CONFIG_POSIX_SIGNALS +#endif + +#if !defined(CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS) +# define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS +# define CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS +#endif +#if !defined(CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS) +# define CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS +# define CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS +#endif + +// end catch_compiler_capabilities.h +#define INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) name##line +#define INTERNAL_CATCH_UNIQUE_NAME_LINE( name, line ) INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) +#ifdef CATCH_CONFIG_COUNTER +# define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __COUNTER__ ) +#else +# define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __LINE__ ) +#endif + +#define INTERNAL_CATCH_STRINGIFY2( expr ) #expr +#define INTERNAL_CATCH_STRINGIFY( expr ) INTERNAL_CATCH_STRINGIFY2( expr ) + +#include +#include +#include + +namespace Catch { + + struct IConfig; + + struct CaseSensitive { enum Choice { + Yes, + No + }; }; + + class NonCopyable { + NonCopyable( NonCopyable const& ) = delete; + NonCopyable( NonCopyable && ) = delete; + NonCopyable& operator = ( NonCopyable const& ) = delete; + NonCopyable& operator = ( NonCopyable && ) = delete; + + protected: + NonCopyable() {} + virtual ~NonCopyable(); + }; + + struct SourceLineInfo { + + SourceLineInfo() = delete; + SourceLineInfo( char const* _file, std::size_t _line ) noexcept; + + SourceLineInfo( SourceLineInfo const& other ) = default; + SourceLineInfo( SourceLineInfo && ) = default; + SourceLineInfo& operator = ( SourceLineInfo const& ) = default; + SourceLineInfo& operator = ( SourceLineInfo && ) = default; + + bool empty() const noexcept; + bool operator == ( SourceLineInfo const& other ) const noexcept; + bool operator < ( SourceLineInfo const& other ) const noexcept; + + char const* file; + std::size_t line; + }; + + std::ostream& operator << ( std::ostream& os, SourceLineInfo const& info ); + + // This is just here to avoid compiler warnings with macro constants and boolean literals + bool isTrue( bool value ); + bool alwaysTrue(); + bool alwaysFalse(); + + void seedRng( IConfig const& config ); + unsigned int rngSeed(); + + // Use this in variadic streaming macros to allow + // >> +StreamEndStop + // as well as + // >> stuff +StreamEndStop + struct StreamEndStop { + std::string operator+() const; + }; + template + T const& operator + ( T const& value, StreamEndStop ) { + return value; + } +} + +#define CATCH_INTERNAL_LINEINFO \ + ::Catch::SourceLineInfo( __FILE__, static_cast( __LINE__ ) ) + +// end catch_common.h +namespace Catch { + + struct RegistrarForTagAliases { + RegistrarForTagAliases( char const* alias, char const* tag, SourceLineInfo const& lineInfo ); + }; + +} // end namespace Catch + +#define CATCH_REGISTER_TAG_ALIAS( alias, spec ) namespace{ Catch::RegistrarForTagAliases INTERNAL_CATCH_UNIQUE_NAME( AutoRegisterTagAlias )( alias, spec, CATCH_INTERNAL_LINEINFO ); } + +// end catch_tag_alias_autoregistrar.h +// start catch_test_registry.hpp + +// start catch_interfaces_testcase.h + +#include +#include + +namespace Catch { + + class TestSpec; + + struct ITestInvoker { + virtual void invoke () const = 0; + virtual ~ITestInvoker(); + }; + + using ITestCasePtr = std::shared_ptr; + + class TestCase; + struct IConfig; + + struct ITestCaseRegistry { + virtual ~ITestCaseRegistry(); + virtual std::vector const& getAllTests() const = 0; + virtual std::vector const& getAllTestsSorted( IConfig const& config ) const = 0; + }; + + bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ); + std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ); + std::vector const& getAllTestCasesSorted( IConfig const& config ); + +} + +// end catch_interfaces_testcase.h +// start catch_stringref.h + +#include +#include +#include + +namespace Catch { + + class StringData; + + /// A non-owning string class (similar to the forthcoming std::string_view) + /// Note that, because a StringRef may be a substring of another string, + /// it may not be null terminated. c_str() must return a null terminated + /// string, however, and so the StringRef will internally take ownership + /// (taking a copy), if necessary. In theory this ownership is not externally + /// visible - but it does mean (substring) StringRefs should not be shared between + /// threads. + class StringRef { + friend struct StringRefTestAccess; + + using size_type = size_t; + + char const* m_start; + size_type m_size; + + char* m_data = nullptr; + + void takeOwnership(); + + public: // construction/ assignment + StringRef() noexcept; + StringRef( StringRef const& other ) noexcept; + StringRef( StringRef&& other ) noexcept; + StringRef( char const* rawChars ) noexcept; + StringRef( char const* rawChars, size_type size ) noexcept; + StringRef( std::string const& stdString ) noexcept; + ~StringRef() noexcept; + + auto operator = ( StringRef other ) noexcept -> StringRef&; + operator std::string() const; + + void swap( StringRef& other ) noexcept; + + public: // operators + auto operator == ( StringRef const& other ) const noexcept -> bool; + auto operator != ( StringRef const& other ) const noexcept -> bool; + + auto operator[] ( size_type index ) const noexcept -> char; + + public: // named queries + auto empty() const noexcept -> bool; + auto size() const noexcept -> size_type; + auto numberOfCharacters() const noexcept -> size_type; + auto c_str() const -> char const*; + + public: // substrings and searches + auto substr( size_type start, size_type size ) const noexcept -> StringRef; + + private: // ownership queries - may not be consistent between calls + auto isOwned() const noexcept -> bool; + auto isSubstring() const noexcept -> bool; + auto data() const noexcept -> char const*; + }; + + auto operator + ( StringRef const& lhs, StringRef const& rhs ) -> std::string; + auto operator + ( StringRef const& lhs, char const* rhs ) -> std::string; + auto operator + ( char const* lhs, StringRef const& rhs ) -> std::string; + + auto operator << ( std::ostream& os, StringRef const& sr ) -> std::ostream&; + +} // namespace Catch + +// end catch_stringref.h +namespace Catch { + +template +class TestInvokerAsMethod : public ITestInvoker { + void (C::*m_testAsMethod)(); +public: + TestInvokerAsMethod( void (C::*testAsMethod)() ) noexcept : m_testAsMethod( testAsMethod ) {} + + void invoke() const override { + C obj; + (obj.*m_testAsMethod)(); + } +}; + +auto makeTestInvoker( void(*testAsFunction)() ) noexcept -> ITestInvoker*; + +template +auto makeTestInvoker( void (C::*testAsMethod)() ) noexcept -> ITestInvoker* { + return new(std::nothrow) TestInvokerAsMethod( testAsMethod ); +} + +struct NameAndTags { + NameAndTags( StringRef name_ = "", StringRef tags_ = "" ) noexcept; + StringRef name; + StringRef tags; +}; + +struct AutoReg : NonCopyable { + AutoReg( ITestInvoker* invoker, SourceLineInfo const& lineInfo, StringRef classOrMethod, NameAndTags const& nameAndTags ) noexcept; + ~AutoReg() = default; +}; + +} // end namespace Catch + + /////////////////////////////////////////////////////////////////////////////// + #define INTERNAL_CATCH_TESTCASE2( TestName, ... ) \ + static void TestName(); \ + CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS \ + namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( Catch::makeTestInvoker( &TestName ), CATCH_INTERNAL_LINEINFO, "", Catch::NameAndTags{ __VA_ARGS__ } ); } /* NOLINT */ \ + CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS \ + static void TestName() + #define INTERNAL_CATCH_TESTCASE( ... ) \ + INTERNAL_CATCH_TESTCASE2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), __VA_ARGS__ ) + + /////////////////////////////////////////////////////////////////////////////// + #define INTERNAL_CATCH_METHOD_AS_TEST_CASE( QualifiedMethod, ... ) \ + CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS \ + namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( Catch::makeTestInvoker( &QualifiedMethod ), CATCH_INTERNAL_LINEINFO, "&" #QualifiedMethod, Catch::NameAndTags{ __VA_ARGS__ } ); } /* NOLINT */ \ + CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS + + /////////////////////////////////////////////////////////////////////////////// + #define INTERNAL_CATCH_TEST_CASE_METHOD2( TestName, ClassName, ... )\ + CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS \ + namespace{ \ + struct TestName : ClassName{ \ + void test(); \ + }; \ + Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( Catch::makeTestInvoker( &TestName::test ), CATCH_INTERNAL_LINEINFO, #ClassName, Catch::NameAndTags{ __VA_ARGS__ } ); /* NOLINT */ \ + } \ + CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS \ + void TestName::test() + #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, ... ) \ + INTERNAL_CATCH_TEST_CASE_METHOD2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), ClassName, __VA_ARGS__ ) + + /////////////////////////////////////////////////////////////////////////////// + #define INTERNAL_CATCH_REGISTER_TESTCASE( Function, ... ) \ + CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS \ + Catch::AutoReg( Catch::makeTestInvoker( Function ), CATCH_INTERNAL_LINEINFO, "", Catch::NameAndTags{ __VA_ARGS__ } ); /* NOLINT */ \ + CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS + +// end catch_test_registry.hpp +// start catch_capture.hpp + +// start catch_assertionhandler.h + +// start catch_decomposer.h + +// start catch_tostring.h + +#include +#include +#include +#include +#include +#include + +#ifdef __OBJC__ +// start catch_objc_arc.hpp + +#import + +#ifdef __has_feature +#define CATCH_ARC_ENABLED __has_feature(objc_arc) +#else +#define CATCH_ARC_ENABLED 0 +#endif + +void arcSafeRelease( NSObject* obj ); +id performOptionalSelector( id obj, SEL sel ); + +#if !CATCH_ARC_ENABLED +inline void arcSafeRelease( NSObject* obj ) { + [obj release]; +} +inline id performOptionalSelector( id obj, SEL sel ) { + if( [obj respondsToSelector: sel] ) + return [obj performSelector: sel]; + return nil; +} +#define CATCH_UNSAFE_UNRETAINED +#define CATCH_ARC_STRONG +#else +inline void arcSafeRelease( NSObject* ){} +inline id performOptionalSelector( id obj, SEL sel ) { +#ifdef __clang__ +#pragma clang diagnostic push +#pragma clang diagnostic ignored "-Warc-performSelector-leaks" +#endif + if( [obj respondsToSelector: sel] ) + return [obj performSelector: sel]; +#ifdef __clang__ +#pragma clang diagnostic pop +#endif + return nil; +} +#define CATCH_UNSAFE_UNRETAINED __unsafe_unretained +#define CATCH_ARC_STRONG __strong +#endif + +// end catch_objc_arc.hpp +#endif + +// We need a dummy global operator<< so we can bring it into Catch namespace later +struct Catch_global_namespace_dummy; +std::ostream& operator<<(std::ostream&, Catch_global_namespace_dummy); + +namespace Catch { + // Bring in operator<< from global namespace into Catch namespace + using ::operator<<; + + namespace Detail { + + extern const std::string unprintableString; + + std::string rawMemoryToString( const void *object, std::size_t size ); + + template + std::string rawMemoryToString( const T& object ) { + return rawMemoryToString( &object, sizeof(object) ); + } + + template + class IsStreamInsertable { + template + static auto test(int) + -> decltype(std::declval() << std::declval(), std::true_type()); + + template + static auto test(...)->std::false_type; + + public: + static const bool value = decltype(test(0))::value; + }; + + } // namespace Detail + + // If we decide for C++14, change these to enable_if_ts + template + struct StringMaker { + template + static + typename std::enable_if<::Catch::Detail::IsStreamInsertable::value, std::string>::type + convert(const Fake& t) { + std::ostringstream sstr; + sstr << t; + return sstr.str(); + } + + template + static + typename std::enable_if::value, std::string>::type + convert(const Fake&) { + return Detail::unprintableString; + } + }; + + namespace Detail { + + // This function dispatches all stringification requests inside of Catch. + // Should be preferably called fully qualified, like ::Catch::Detail::stringify + template + std::string stringify(const T& e) { + return ::Catch::StringMaker::type>::type>::convert(e); + } + + } // namespace Detail + + // Some predefined specializations + + template<> + struct StringMaker { + static std::string convert(const std::string& str); + }; + template<> + struct StringMaker { + static std::string convert(const std::wstring& wstr); + }; + + template<> + struct StringMaker { + static std::string convert(char const * str); + }; + template<> + struct StringMaker { + static std::string convert(char * str); + }; + template<> + struct StringMaker { + static std::string convert(wchar_t const * str); + }; + template<> + struct StringMaker { + static std::string convert(wchar_t * str); + }; + + template + struct StringMaker { + static std::string convert(const char* str) { + return ::Catch::Detail::stringify(std::string{ str }); + } + }; + template + struct StringMaker { + static std::string convert(const char* str) { + return ::Catch::Detail::stringify(std::string{ str }); + } + }; + template + struct StringMaker { + static std::string convert(const char* str) { + return ::Catch::Detail::stringify(std::string{ str }); + } + }; + + template<> + struct StringMaker { + static std::string convert(int value); + }; + template<> + struct StringMaker { + static std::string convert(long value); + }; + template<> + struct StringMaker { + static std::string convert(long long value); + }; + template<> + struct StringMaker { + static std::string convert(unsigned int value); + }; + template<> + struct StringMaker { + static std::string convert(unsigned long value); + }; + template<> + struct StringMaker { + static std::string convert(unsigned long long value); + }; + + template<> + struct StringMaker { + static std::string convert(bool b); + }; + + template<> + struct StringMaker { + static std::string convert(char c); + }; + template<> + struct StringMaker { + static std::string convert(signed char c); + }; + template<> + struct StringMaker { + static std::string convert(unsigned char c); + }; + + template<> + struct StringMaker { + static std::string convert(std::nullptr_t); + }; + + template<> + struct StringMaker { + static std::string convert(float value); + }; + template<> + struct StringMaker { + static std::string convert(double value); + }; + + template + struct StringMaker { + template + static std::string convert(U* p) { + if (p) { + return ::Catch::Detail::rawMemoryToString(p); + } else { + return "nullptr"; + } + } + }; + + template + struct StringMaker { + static std::string convert(R C::* p) { + if (p) { + return ::Catch::Detail::rawMemoryToString(p); + } else { + return "nullptr"; + } + } + }; + + namespace Detail { + template + std::string rangeToString(InputIterator first, InputIterator last) { + std::ostringstream oss; + oss << "{ "; + if (first != last) { + oss << ::Catch::Detail::stringify(*first); + for (++first; first != last; ++first) + oss << ", " << ::Catch::Detail::stringify(*first); + } + oss << " }"; + return oss.str(); + } + } + + template + struct StringMaker > { + static std::string convert( std::vector const& v ) { + return ::Catch::Detail::rangeToString( v.begin(), v.end() ); + } + }; + + // === Pair === + template + struct StringMaker > { + static std::string convert(const std::pair& pair) { + std::ostringstream oss; + oss << "{ " + << ::Catch::Detail::stringify(pair.first) + << ", " + << ::Catch::Detail::stringify(pair.second) + << " }"; + return oss.str(); + } + }; + + namespace Detail { + template< + typename Tuple, + std::size_t N = 0, + bool = (N < std::tuple_size::value) + > + struct TupleElementPrinter { + static void print(const Tuple& tuple, std::ostream& os) { + os << (N ? ", " : " ") + << ::Catch::Detail::stringify(std::get(tuple)); + TupleElementPrinter::print(tuple, os); + } + }; + + template< + typename Tuple, + std::size_t N + > + struct TupleElementPrinter { + static void print(const Tuple&, std::ostream&) {} + }; + + } + + template + struct StringMaker> { + static std::string convert(const std::tuple& tuple) { + std::ostringstream os; + os << '{'; + Detail::TupleElementPrinter>::print(tuple, os); + os << " }"; + return os.str(); + } + }; + + template + struct EnumStringMaker { + static std::string convert(const T& t) { + return ::Catch::Detail::stringify(static_cast::type>(t)); + } + }; + +#ifdef __OBJC__ + template<> + struct StringMaker { + static std::string convert(NSString* nsstring); + }; + template<> + struct StringMaker { + static std::string convert(NSString * CATCH_ARC_STRONG nsstring); + }; + template<> + struct StringMaker { + static std::string convert(NSObject* nsObject); + }; +#endif + +} // namespace Catch + +// end catch_tostring.h +#include + +#ifdef _MSC_VER +#pragma warning(push) +#pragma warning(disable:4389) // '==' : signed/unsigned mismatch +#pragma warning(disable:4018) // more "signed/unsigned mismatch" +#pragma warning(disable:4312) // Converting int to T* using reinterpret_cast (issue on x64 platform) +#endif + +namespace Catch { + + struct ITransientExpression { + virtual auto isBinaryExpression() const -> bool = 0; + virtual auto getResult() const -> bool = 0; + virtual void streamReconstructedExpression( std::ostream &os ) const = 0; + + // We don't actually need a virtual destructore, but many static analysers + // complain if it's not here :-( + virtual ~ITransientExpression() = default; + }; + + void formatReconstructedExpression( std::ostream &os, std::string const& lhs, std::string const& op, std::string const& rhs ); + + template + class BinaryExpr : public ITransientExpression { + bool m_result; + LhsT m_lhs; + std::string m_op; + RhsT m_rhs; + + auto isBinaryExpression() const -> bool override { return true; } + auto getResult() const -> bool override { return m_result; } + + void streamReconstructedExpression( std::ostream &os ) const override { + formatReconstructedExpression + ( os, Catch::Detail::stringify( m_lhs ), m_op, Catch::Detail::stringify( m_rhs ) ); + } + + public: + BinaryExpr( bool comparisionResult, LhsT lhs, StringRef op, RhsT rhs ) + : m_result( comparisionResult ), + m_lhs( lhs ), + m_op( op ), + m_rhs( rhs ) + {} + }; + + template + class UnaryExpr : public ITransientExpression { + LhsT m_lhs; + + auto isBinaryExpression() const -> bool override { return false; } + auto getResult() const -> bool override { return m_lhs ? true : false; } + + void streamReconstructedExpression( std::ostream &os ) const override { + os << Catch::Detail::stringify( m_lhs ); + } + + public: + UnaryExpr( LhsT lhs ) : m_lhs( lhs ) {} + }; + + // Specialised comparison functions to handle equality comparisons between ints and pointers (NULL deduces as an int) + template + auto compareEqual( LhsT const& lhs, RhsT&& rhs ) -> bool { return const_cast( lhs ) == rhs; }; + template + auto compareEqual( T* const& lhs, int rhs ) -> bool { return lhs == reinterpret_cast( rhs ); }; + template + auto compareEqual( int lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) == rhs; }; + + template + auto compareNotEqual( LhsT const& lhs, RhsT&& rhs ) -> bool { return const_cast( lhs ) != rhs; }; + template + auto compareNotEqual( T* const& lhs, int rhs ) -> bool { return lhs != reinterpret_cast( rhs ); }; + template + auto compareNotEqual( int lhs, T* const& rhs ) -> bool { return reinterpret_cast( lhs ) != rhs; }; + + template + class ExprLhs { + LhsT m_lhs; + public: + ExprLhs( LhsT lhs ) : m_lhs( lhs ) {} + + template + auto operator == ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( compareEqual( m_lhs, rhs ), m_lhs, "==", rhs ); + } + auto operator == ( bool rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs == rhs, m_lhs, "==", rhs ); + } + + template + auto operator != ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( compareNotEqual( m_lhs, rhs ), m_lhs, "!=", rhs ); + } + auto operator != ( bool rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs != rhs, m_lhs, "!=", rhs ); + } + + template + auto operator > ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs > rhs, m_lhs, ">", rhs ); + } + template + auto operator < ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs < rhs, m_lhs, "<", rhs ); + } + template + auto operator >= ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs >= rhs, m_lhs, ">=", rhs ); + } + template + auto operator <= ( RhsT&& rhs ) -> BinaryExpr const { + return BinaryExpr( m_lhs <= rhs, m_lhs, "<=", rhs ); + } + + auto makeUnaryExpr() const -> UnaryExpr { + return UnaryExpr( m_lhs ); + } + }; + + void handleExpression( ITransientExpression const& expr ); + + template + void handleExpression( ExprLhs const& expr ) { + handleExpression( expr.makeUnaryExpr() ); + } + + struct Decomposer { + template + auto operator <= ( T& lhs ) -> ExprLhs { + return ExprLhs( lhs ); + } + template + auto operator <= ( T const& lhs ) -> ExprLhs { + return ExprLhs( lhs ); + } + auto operator <=( bool value ) -> ExprLhs { + return ExprLhs( value ); + } + }; + +} // end namespace Catch + +#ifdef _MSC_VER +#pragma warning(pop) +#endif + +// end catch_decomposer.h +// start catch_assertioninfo.h + +// start catch_result_type.h + +namespace Catch { + + // ResultWas::OfType enum + struct ResultWas { enum OfType { + Unknown = -1, + Ok = 0, + Info = 1, + Warning = 2, + + FailureBit = 0x10, + + ExpressionFailed = FailureBit | 1, + ExplicitFailure = FailureBit | 2, + + Exception = 0x100 | FailureBit, + + ThrewException = Exception | 1, + DidntThrowException = Exception | 2, + + FatalErrorCondition = 0x200 | FailureBit + + }; }; + + bool isOk( ResultWas::OfType resultType ); + bool isJustInfo( int flags ); + + // ResultDisposition::Flags enum + struct ResultDisposition { enum Flags { + Normal = 0x01, + + ContinueOnFailure = 0x02, // Failures fail test, but execution continues + FalseTest = 0x04, // Prefix expression with ! + SuppressFail = 0x08 // Failures are reported but do not fail the test + }; }; + + ResultDisposition::Flags operator | ( ResultDisposition::Flags lhs, ResultDisposition::Flags rhs ); + + bool shouldContinueOnFailure( int flags ); + bool isFalseTest( int flags ); + bool shouldSuppressFailure( int flags ); + +} // end namespace Catch + +// end catch_result_type.h +namespace Catch { + + struct AssertionInfo + { + StringRef macroName; + SourceLineInfo lineInfo; + StringRef capturedExpression; + ResultDisposition::Flags resultDisposition; + + // We want to delete this constructor but a compiler bug in 4.8 means + // the struct is then treated as non-aggregate + //AssertionInfo() = delete; + }; + +} // end namespace Catch + +// end catch_assertioninfo.h +namespace Catch { + + struct TestFailureException{}; + struct AssertionResultData; + + class LazyExpression { + friend class AssertionHandler; + friend struct AssertionStats; + + ITransientExpression const* m_transientExpression = nullptr; + bool m_isNegated; + public: + LazyExpression( bool isNegated ); + LazyExpression( LazyExpression const& other ); + LazyExpression& operator = ( LazyExpression const& ) = delete; + + explicit operator bool() const; + + friend auto operator << ( std::ostream& os, LazyExpression const& lazyExpr ) -> std::ostream&; + }; + + class AssertionHandler { + AssertionInfo m_assertionInfo; + bool m_shouldDebugBreak = false; + bool m_shouldThrow = false; + bool m_inExceptionGuard = false; + + public: + AssertionHandler + ( StringRef macroName, + SourceLineInfo const& lineInfo, + StringRef capturedExpression, + ResultDisposition::Flags resultDisposition ); + ~AssertionHandler(); + + void handle( ITransientExpression const& expr ); + + template + void handle( ExprLhs const& expr ) { + handle( expr.makeUnaryExpr() ); + } + void handle( ResultWas::OfType resultType ); + void handle( ResultWas::OfType resultType, StringRef const& message ); + void handle( ResultWas::OfType resultType, ITransientExpression const* expr, bool negated ); + void handle( AssertionResultData const& resultData, ITransientExpression const* expr ); + + auto shouldDebugBreak() const -> bool; + auto allowThrows() const -> bool; + void reactWithDebugBreak() const; + void reactWithoutDebugBreak() const; + void useActiveException(); + void setExceptionGuard(); + void unsetExceptionGuard(); + }; + + void handleExceptionMatchExpr( AssertionHandler& handler, std::string const& str, StringRef matcherString ); + +} // namespace Catch + +// end catch_assertionhandler.h +// start catch_message.h + +#include +#include + +namespace Catch { + + struct MessageInfo { + MessageInfo( std::string const& _macroName, + SourceLineInfo const& _lineInfo, + ResultWas::OfType _type ); + + std::string macroName; + SourceLineInfo lineInfo; + ResultWas::OfType type; + std::string message; + unsigned int sequence; + + bool operator == ( MessageInfo const& other ) const; + bool operator < ( MessageInfo const& other ) const; + private: + static unsigned int globalCount; + }; + + struct MessageStream { + + template + MessageStream& operator << ( T const& value ) { + m_stream << value; + return *this; + } + + // !TBD reuse a global/ thread-local stream + std::ostringstream m_stream; + }; + + struct MessageBuilder : MessageStream { + MessageBuilder( std::string const& macroName, + SourceLineInfo const& lineInfo, + ResultWas::OfType type ); + + template + MessageBuilder& operator << ( T const& value ) { + m_stream << value; + return *this; + } + + MessageInfo m_info; + }; + + class ScopedMessage { + public: + ScopedMessage( MessageBuilder const& builder ); + ~ScopedMessage(); + + MessageInfo m_info; + }; + +} // end namespace Catch + +// end catch_message.h +// start catch_interfaces_capture.h + +#include + +namespace Catch { + + class TestCase; + class AssertionResult; + struct AssertionInfo; + struct SectionInfo; + struct SectionEndInfo; + struct MessageInfo; + class ScopedMessageBuilder; + struct Counts; + struct BenchmarkInfo; + struct BenchmarkStats; + + struct IResultCapture { + + virtual ~IResultCapture(); + + virtual void assertionStarting( AssertionInfo const& info ) = 0; + virtual void assertionEnded( AssertionResult const& result ) = 0; + virtual bool sectionStarted( SectionInfo const& sectionInfo, + Counts& assertions ) = 0; + virtual void sectionEnded( SectionEndInfo const& endInfo ) = 0; + virtual void sectionEndedEarly( SectionEndInfo const& endInfo ) = 0; + + virtual void benchmarkStarting( BenchmarkInfo const& info ) = 0; + virtual void benchmarkEnded( BenchmarkStats const& stats ) = 0; + + virtual void pushScopedMessage( MessageInfo const& message ) = 0; + virtual void popScopedMessage( MessageInfo const& message ) = 0; + + virtual std::string getCurrentTestName() const = 0; + virtual const AssertionResult* getLastResult() const = 0; + + virtual void exceptionEarlyReported() = 0; + + virtual void handleFatalErrorCondition( std::string const& message ) = 0; + + virtual bool lastAssertionPassed() = 0; + virtual void assertionPassed() = 0; + virtual void assertionRun() = 0; + }; + + IResultCapture& getResultCapture(); +} + +// end catch_interfaces_capture.h +#if defined(CATCH_CONFIG_FAST_COMPILE) +/////////////////////////////////////////////////////////////////////////////// +// We can speedup compilation significantly by breaking into debugger lower in +// the callstack, because then we don't have to expand CATCH_BREAK_INTO_DEBUGGER +// macro in each assertion +#define INTERNAL_CATCH_REACT( handler ) \ + handler.reactWithDebugBreak(); + +/////////////////////////////////////////////////////////////////////////////// +// Another way to speed-up compilation is to omit local try-catch for REQUIRE* +// macros. +// This can potentially cause false negative, if the test code catches +// the exception before it propagates back up to the runner. +#define INTERNAL_CATCH_TRY( capturer ) capturer.setExceptionGuard(); +#define INTERNAL_CATCH_CATCH( capturer ) capturer.unsetExceptionGuard(); + +#else // CATCH_CONFIG_FAST_COMPILE + +// start catch_debugger.h + +// start catch_platform.h + +#ifdef __APPLE__ +# include +# if TARGET_OS_MAC == 1 +# define CATCH_PLATFORM_MAC +# elif TARGET_OS_IPHONE == 1 +# define CATCH_PLATFORM_IPHONE +# endif + +#elif defined(linux) || defined(__linux) || defined(__linux__) +# define CATCH_PLATFORM_LINUX + +#elif defined(WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_MSC_VER) +# define CATCH_PLATFORM_WINDOWS +#endif + +// end catch_platform.h +#include + +namespace Catch{ + + bool isDebuggerActive(); + void writeToDebugConsole( std::string const& text ); +} + +#ifdef CATCH_PLATFORM_MAC + + #define CATCH_TRAP() __asm__("int $3\n" : : ) /* NOLINT */ + +#elif defined(CATCH_PLATFORM_LINUX) + // If we can use inline assembler, do it because this allows us to break + // directly at the location of the failing check instead of breaking inside + // raise() called from it, i.e. one stack frame below. + #if defined(__GNUC__) && (defined(__i386) || defined(__x86_64)) + #define CATCH_TRAP() asm volatile ("int $3") /* NOLINT */ + #else // Fall back to the generic way. + #include + + #define CATCH_TRAP() raise(SIGTRAP) + #endif +#elif defined(_MSC_VER) + #define CATCH_TRAP() __debugbreak() +#elif defined(__MINGW32__) + extern "C" __declspec(dllimport) void __stdcall DebugBreak(); + #define CATCH_TRAP() DebugBreak() +#endif + +#ifdef CATCH_TRAP + #define CATCH_BREAK_INTO_DEBUGGER() if( Catch::isDebuggerActive() ) { CATCH_TRAP(); } +#else + #define CATCH_BREAK_INTO_DEBUGGER() Catch::alwaysTrue(); +#endif + +// end catch_debugger.h +/////////////////////////////////////////////////////////////////////////////// +// In the event of a failure works out if the debugger needs to be invoked +// and/or an exception thrown and takes appropriate action. +// This needs to be done as a macro so the debugger will stop in the user +// source code rather than in Catch library code +#define INTERNAL_CATCH_REACT( handler ) \ + if( handler.shouldDebugBreak() ) CATCH_BREAK_INTO_DEBUGGER(); \ + handler.reactWithoutDebugBreak(); + +#define INTERNAL_CATCH_TRY( capturer ) try +#define INTERNAL_CATCH_CATCH( capturer ) catch(...) { capturer.useActiveException(); } + +#endif + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_TEST( macroName, resultDisposition, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #__VA_ARGS__, resultDisposition ); \ + INTERNAL_CATCH_TRY( catchAssertionHandler ) { \ + CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS \ + catchAssertionHandler.handle( Catch::Decomposer() <= __VA_ARGS__ ); \ + CATCH_INTERNAL_UNSUPPRESS_PARENTHESES_WARNINGS \ + } INTERNAL_CATCH_CATCH( catchAssertionHandler ) \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::isTrue( false && static_cast( !!(__VA_ARGS__) ) ) ) // the expression here is never evaluated at runtime but it forces the compiler to give it a look + // The double negation silences MSVC's C4800 warning, the static_cast forces short-circuit evaluation if the type has overloaded &&. + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_IF( macroName, resultDisposition, ... ) \ + INTERNAL_CATCH_TEST( macroName, resultDisposition, __VA_ARGS__ ); \ + if( Catch::getResultCapture().lastAssertionPassed() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_ELSE( macroName, resultDisposition, ... ) \ + INTERNAL_CATCH_TEST( macroName, resultDisposition, __VA_ARGS__ ); \ + if( !Catch::getResultCapture().lastAssertionPassed() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_NO_THROW( macroName, resultDisposition, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #__VA_ARGS__, resultDisposition ); \ + try { \ + static_cast(__VA_ARGS__); \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + } \ + catch( ... ) { \ + catchAssertionHandler.useActiveException(); \ + } \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_THROWS( macroName, resultDisposition, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #__VA_ARGS__, resultDisposition); \ + if( catchAssertionHandler.allowThrows() ) \ + try { \ + static_cast(__VA_ARGS__); \ + catchAssertionHandler.handle( Catch::ResultWas::DidntThrowException ); \ + } \ + catch( ... ) { \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + } \ + else \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_THROWS_AS( macroName, exceptionType, resultDisposition, expr ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #expr ", " #exceptionType, resultDisposition ); \ + if( catchAssertionHandler.allowThrows() ) \ + try { \ + static_cast(expr); \ + catchAssertionHandler.handle( Catch::ResultWas::DidntThrowException ); \ + } \ + catch( exceptionType const& ) { \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + } \ + catch( ... ) { \ + catchAssertionHandler.useActiveException(); \ + } \ + else \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_MSG( macroName, messageType, resultDisposition, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, "", resultDisposition ); \ + catchAssertionHandler.handle( messageType, ( Catch::MessageStream() << __VA_ARGS__ + ::Catch::StreamEndStop() ).m_stream.str() ); \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_INFO( macroName, log ) \ + Catch::ScopedMessage INTERNAL_CATCH_UNIQUE_NAME( scopedMessage ) = Catch::MessageBuilder( macroName, CATCH_INTERNAL_LINEINFO, Catch::ResultWas::Info ) << log; + +/////////////////////////////////////////////////////////////////////////////// +// Although this is matcher-based, it can be used with just a string +#define INTERNAL_CATCH_THROWS_STR_MATCHES( macroName, resultDisposition, matcher, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #__VA_ARGS__ ", " #matcher, resultDisposition ); \ + if( catchAssertionHandler.allowThrows() ) \ + try { \ + static_cast(__VA_ARGS__); \ + catchAssertionHandler.handle( Catch::ResultWas::DidntThrowException ); \ + } \ + catch( ... ) { \ + handleExceptionMatchExpr( catchAssertionHandler, matcher, #matcher ); \ + } \ + else \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +// end catch_capture.hpp +// start catch_section.h + +// start catch_section_info.h + +// start catch_totals.hpp + +#include + +namespace Catch { + + struct Counts { + Counts operator - ( Counts const& other ) const; + Counts& operator += ( Counts const& other ); + + std::size_t total() const; + bool allPassed() const; + bool allOk() const; + + std::size_t passed = 0; + std::size_t failed = 0; + std::size_t failedButOk = 0; + }; + + struct Totals { + + Totals operator - ( Totals const& other ) const; + Totals& operator += ( Totals const& other ); + + Totals delta( Totals const& prevTotals ) const; + + Counts assertions; + Counts testCases; + }; +} + +// end catch_totals.hpp +#include + +namespace Catch { + + struct SectionInfo { + SectionInfo + ( SourceLineInfo const& _lineInfo, + std::string const& _name, + std::string const& _description = std::string() ); + + std::string name; + std::string description; + SourceLineInfo lineInfo; + }; + + struct SectionEndInfo { + SectionEndInfo( SectionInfo const& _sectionInfo, Counts const& _prevAssertions, double _durationInSeconds ); + + SectionInfo sectionInfo; + Counts prevAssertions; + double durationInSeconds; + }; + +} // end namespace Catch + +// end catch_section_info.h +// start catch_timer.h + +#include + +namespace Catch { + + auto getCurrentNanosecondsSinceEpoch() -> uint64_t; + auto getEstimatedClockResolution() -> uint64_t; + + class Timer { + uint64_t m_nanoseconds = 0; + public: + void start(); + auto getElapsedNanoseconds() const -> unsigned int; + auto getElapsedMicroseconds() const -> unsigned int; + auto getElapsedMilliseconds() const -> unsigned int; + auto getElapsedSeconds() const -> double; + }; + +} // namespace Catch + +// end catch_timer.h +#include + +namespace Catch { + + class Section : NonCopyable { + public: + Section( SectionInfo const& info ); + ~Section(); + + // This indicates whether the section should be executed or not + explicit operator bool() const; + + private: + SectionInfo m_info; + + std::string m_name; + Counts m_assertions; + bool m_sectionIncluded; + Timer m_timer; + }; + +} // end namespace Catch + + #define INTERNAL_CATCH_SECTION( ... ) \ + if( Catch::Section const& INTERNAL_CATCH_UNIQUE_NAME( catch_internal_Section ) = Catch::SectionInfo( CATCH_INTERNAL_LINEINFO, __VA_ARGS__ ) ) + +// end catch_section.h +// start catch_benchmark.h + +#include +#include + +namespace Catch { + + class BenchmarkLooper { + + std::string m_name; + size_t m_count = 0; + size_t m_iterationsToRun = 1; + uint64_t m_resolution; + Timer m_timer; + + static auto getResolution() -> uint64_t; + public: + // Keep most of this inline as it's on the code path that is being timed + BenchmarkLooper( StringRef name ) + : m_name( name ), + m_resolution( getResolution() ) + { + reportStart(); + m_timer.start(); + } + + explicit operator bool() { + if( m_count < m_iterationsToRun ) + return true; + return needsMoreIterations(); + } + + void increment() { + ++m_count; + } + + void reportStart(); + auto needsMoreIterations() -> bool; + }; + +} // end namespace Catch + +#define BENCHMARK( name ) \ + for( Catch::BenchmarkLooper looper( name ); looper; looper.increment() ) + +// end catch_benchmark.h +// start catch_interfaces_exception.h + +#include +#include + +// start catch_interfaces_registry_hub.h + +#include +#include + +namespace Catch { + + class TestCase; + struct ITestCaseRegistry; + struct IExceptionTranslatorRegistry; + struct IExceptionTranslator; + struct IReporterRegistry; + struct IReporterFactory; + struct ITagAliasRegistry; + class StartupExceptionRegistry; + + using IReporterFactoryPtr = std::shared_ptr; + + struct IRegistryHub { + virtual ~IRegistryHub(); + + virtual IReporterRegistry const& getReporterRegistry() const = 0; + virtual ITestCaseRegistry const& getTestCaseRegistry() const = 0; + virtual ITagAliasRegistry const& getTagAliasRegistry() const = 0; + + virtual IExceptionTranslatorRegistry& getExceptionTranslatorRegistry() = 0; + + virtual StartupExceptionRegistry const& getStartupExceptionRegistry() const = 0; + }; + + struct IMutableRegistryHub { + virtual ~IMutableRegistryHub(); + virtual void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) = 0; + virtual void registerListener( IReporterFactoryPtr const& factory ) = 0; + virtual void registerTest( TestCase const& testInfo ) = 0; + virtual void registerTranslator( const IExceptionTranslator* translator ) = 0; + virtual void registerTagAlias( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) = 0; + virtual void registerStartupException() noexcept = 0; + }; + + IRegistryHub& getRegistryHub(); + IMutableRegistryHub& getMutableRegistryHub(); + void cleanUp(); + std::string translateActiveException(); + +} + +// end catch_interfaces_registry_hub.h +namespace Catch { + using exceptionTranslateFunction = std::string(*)(); + + struct IExceptionTranslator; + using ExceptionTranslators = std::vector>; + + struct IExceptionTranslator { + virtual ~IExceptionTranslator(); + virtual std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const = 0; + }; + + struct IExceptionTranslatorRegistry { + virtual ~IExceptionTranslatorRegistry(); + + virtual std::string translateActiveException() const = 0; + }; + + class ExceptionTranslatorRegistrar { + template + class ExceptionTranslator : public IExceptionTranslator { + public: + + ExceptionTranslator( std::string(*translateFunction)( T& ) ) + : m_translateFunction( translateFunction ) + {} + + std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const override { + try { + if( it == itEnd ) + throw; + else + return (*it)->translate( it+1, itEnd ); + } + catch( T& ex ) { + return m_translateFunction( ex ); + } + } + + protected: + std::string(*m_translateFunction)( T& ); + }; + + public: + template + ExceptionTranslatorRegistrar( std::string(*translateFunction)( T& ) ) { + getMutableRegistryHub().registerTranslator + ( new ExceptionTranslator( translateFunction ) ); + } + }; +} + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_TRANSLATE_EXCEPTION2( translatorName, signature ) \ + static std::string translatorName( signature ); \ + namespace{ Catch::ExceptionTranslatorRegistrar INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionRegistrar )( &translatorName ); }\ + static std::string translatorName( signature ) + +#define INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION2( INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator ), signature ) + +// end catch_interfaces_exception.h +// start catch_approx.hpp + +#include + +#include + +namespace Catch { +namespace Detail { + + double max(double lhs, double rhs); + + class Approx { + public: + explicit Approx ( double value ); + + static Approx custom(); + + template ::value>::type> + Approx operator()( T const& value ) { + Approx approx( static_cast(value) ); + approx.epsilon( m_epsilon ); + approx.margin( m_margin ); + approx.scale( m_scale ); + return approx; + } + + template ::value>::type> + explicit Approx( T const& value ): Approx(static_cast(value)) + {} + + template ::value>::type> + friend bool operator == ( const T& lhs, Approx const& rhs ) { + // Thanks to Richard Harris for his help refining this formula + auto lhs_v = static_cast(lhs); + bool relativeOK = std::fabs(lhs_v - rhs.m_value) < rhs.m_epsilon * (rhs.m_scale + (max)(std::fabs(lhs_v), std::fabs(rhs.m_value))); + if (relativeOK) { + return true; + } + return std::fabs(lhs_v - rhs.m_value) < rhs.m_margin; + } + + template ::value>::type> + friend bool operator == ( Approx const& lhs, const T& rhs ) { + return operator==( rhs, lhs ); + } + + template ::value>::type> + friend bool operator != ( T const& lhs, Approx const& rhs ) { + return !operator==( lhs, rhs ); + } + + template ::value>::type> + friend bool operator != ( Approx const& lhs, T const& rhs ) { + return !operator==( rhs, lhs ); + } + + template ::value>::type> + friend bool operator <= ( T const& lhs, Approx const& rhs ) { + return static_cast(lhs) < rhs.m_value || lhs == rhs; + } + + template ::value>::type> + friend bool operator <= ( Approx const& lhs, T const& rhs ) { + return lhs.m_value < static_cast(rhs) || lhs == rhs; + } + + template ::value>::type> + friend bool operator >= ( T const& lhs, Approx const& rhs ) { + return static_cast(lhs) > rhs.m_value || lhs == rhs; + } + + template ::value>::type> + friend bool operator >= ( Approx const& lhs, T const& rhs ) { + return lhs.m_value > static_cast(rhs) || lhs == rhs; + } + + template ::value>::type> + Approx& epsilon( T const& newEpsilon ) { + m_epsilon = static_cast(newEpsilon); + return *this; + } + + template ::value>::type> + Approx& margin( T const& newMargin ) { + m_margin = static_cast(newMargin); + return *this; + } + + template ::value>::type> + Approx& scale( T const& newScale ) { + m_scale = static_cast(newScale); + return *this; + } + + std::string toString() const; + + private: + double m_epsilon; + double m_margin; + double m_scale; + double m_value; + }; +} + +template<> +struct StringMaker { + static std::string convert(Catch::Detail::Approx const& value); +}; + +} // end namespace Catch + +// end catch_approx.hpp +// start catch_interfaces_tag_alias_registry.h + +#include + +namespace Catch { + + struct TagAlias; + + struct ITagAliasRegistry { + virtual ~ITagAliasRegistry(); + // Nullptr if not present + virtual TagAlias const* find( std::string const& alias ) const = 0; + virtual std::string expandAliases( std::string const& unexpandedTestSpec ) const = 0; + + static ITagAliasRegistry const& get(); + }; + +} // end namespace Catch + +// end catch_interfaces_tag_alias_registry.h +#ifndef CATCH_CONFIG_DISABLE_MATCHERS +// start catch_capture_matchers.h + +// start catch_matchers.hpp + +#include +#include + +namespace Catch { +namespace Matchers { + namespace Impl { + + template struct MatchAllOf; + template struct MatchAnyOf; + template struct MatchNotOf; + + class MatcherUntypedBase { + public: + MatcherUntypedBase() = default; + MatcherUntypedBase ( MatcherUntypedBase const& ) = default; + MatcherUntypedBase& operator = ( MatcherUntypedBase const& ) = delete; + std::string toString() const; + + protected: + virtual ~MatcherUntypedBase() = default; + virtual std::string describe() const = 0; + mutable std::string m_cachedToString; + }; + + template + struct MatcherMethod { + virtual bool match( ObjectT const& arg ) const = 0; + }; + template + struct MatcherMethod { + virtual bool match( PtrT* arg ) const = 0; + }; + + template + struct MatcherBase : MatcherUntypedBase, MatcherMethod { + + MatchAllOf operator && ( MatcherBase const& other ) const; + MatchAnyOf operator || ( MatcherBase const& other ) const; + MatchNotOf operator ! () const; + }; + + template + struct MatchAllOf : MatcherBase { + bool match( ArgT const& arg ) const override { + for( auto matcher : m_matchers ) { + if (!matcher->match(arg)) + return false; + } + return true; + } + std::string describe() const override { + std::string description; + description.reserve( 4 + m_matchers.size()*32 ); + description += "( "; + bool first = true; + for( auto matcher : m_matchers ) { + if( first ) + first = false; + else + description += " and "; + description += matcher->toString(); + } + description += " )"; + return description; + } + + MatchAllOf& operator && ( MatcherBase const& other ) { + m_matchers.push_back( &other ); + return *this; + } + + std::vector const*> m_matchers; + }; + template + struct MatchAnyOf : MatcherBase { + + bool match( ArgT const& arg ) const override { + for( auto matcher : m_matchers ) { + if (matcher->match(arg)) + return true; + } + return false; + } + std::string describe() const override { + std::string description; + description.reserve( 4 + m_matchers.size()*32 ); + description += "( "; + bool first = true; + for( auto matcher : m_matchers ) { + if( first ) + first = false; + else + description += " or "; + description += matcher->toString(); + } + description += " )"; + return description; + } + + MatchAnyOf& operator || ( MatcherBase const& other ) { + m_matchers.push_back( &other ); + return *this; + } + + std::vector const*> m_matchers; + }; + + template + struct MatchNotOf : MatcherBase { + + MatchNotOf( MatcherBase const& underlyingMatcher ) : m_underlyingMatcher( underlyingMatcher ) {} + + bool match( ArgT const& arg ) const override { + return !m_underlyingMatcher.match( arg ); + } + + std::string describe() const override { + return "not " + m_underlyingMatcher.toString(); + } + MatcherBase const& m_underlyingMatcher; + }; + + template + MatchAllOf MatcherBase::operator && ( MatcherBase const& other ) const { + return MatchAllOf() && *this && other; + } + template + MatchAnyOf MatcherBase::operator || ( MatcherBase const& other ) const { + return MatchAnyOf() || *this || other; + } + template + MatchNotOf MatcherBase::operator ! () const { + return MatchNotOf( *this ); + } + + } // namespace Impl + + // The following functions create the actual matcher objects. + // This allows the types to be inferred + // - deprecated: prefer ||, && and ! + template + Impl::MatchNotOf Not( Impl::MatcherBase const& underlyingMatcher ) { + return Impl::MatchNotOf( underlyingMatcher ); + } + template + Impl::MatchAllOf AllOf( Impl::MatcherBase const& m1, Impl::MatcherBase const& m2 ) { + return Impl::MatchAllOf() && m1 && m2; + } + template + Impl::MatchAllOf AllOf( Impl::MatcherBase const& m1, Impl::MatcherBase const& m2, Impl::MatcherBase const& m3 ) { + return Impl::MatchAllOf() && m1 && m2 && m3; + } + template + Impl::MatchAnyOf AnyOf( Impl::MatcherBase const& m1, Impl::MatcherBase const& m2 ) { + return Impl::MatchAnyOf() || m1 || m2; + } + template + Impl::MatchAnyOf AnyOf( Impl::MatcherBase const& m1, Impl::MatcherBase const& m2, Impl::MatcherBase const& m3 ) { + return Impl::MatchAnyOf() || m1 || m2 || m3; + } + +} // namespace Matchers + +using namespace Matchers; +using Matchers::Impl::MatcherBase; + +} // namespace Catch + +// end catch_matchers.hpp +// start catch_matchers_string.h + +#include + +namespace Catch { +namespace Matchers { + + namespace StdString { + + struct CasedString + { + CasedString( std::string const& str, CaseSensitive::Choice caseSensitivity ); + std::string adjustString( std::string const& str ) const; + std::string caseSensitivitySuffix() const; + + CaseSensitive::Choice m_caseSensitivity; + std::string m_str; + }; + + struct StringMatcherBase : MatcherBase { + StringMatcherBase( std::string const& operation, CasedString const& comparator ); + std::string describe() const override; + + CasedString m_comparator; + std::string m_operation; + }; + + struct EqualsMatcher : StringMatcherBase { + EqualsMatcher( CasedString const& comparator ); + bool match( std::string const& source ) const override; + }; + struct ContainsMatcher : StringMatcherBase { + ContainsMatcher( CasedString const& comparator ); + bool match( std::string const& source ) const override; + }; + struct StartsWithMatcher : StringMatcherBase { + StartsWithMatcher( CasedString const& comparator ); + bool match( std::string const& source ) const override; + }; + struct EndsWithMatcher : StringMatcherBase { + EndsWithMatcher( CasedString const& comparator ); + bool match( std::string const& source ) const override; + }; + + } // namespace StdString + + // The following functions create the actual matcher objects. + // This allows the types to be inferred + + StdString::EqualsMatcher Equals( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); + StdString::ContainsMatcher Contains( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); + StdString::EndsWithMatcher EndsWith( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); + StdString::StartsWithMatcher StartsWith( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ); + +} // namespace Matchers +} // namespace Catch + +// end catch_matchers_string.h +// start catch_matchers_vector.h + +namespace Catch { +namespace Matchers { + + namespace Vector { + + template + struct ContainsElementMatcher : MatcherBase, T> { + + ContainsElementMatcher(T const &comparator) : m_comparator( comparator) {} + + bool match(std::vector const &v) const override { + for (auto const& el : v) { + if (el == m_comparator) { + return true; + } + } + return false; + } + + std::string describe() const override { + return "Contains: " + ::Catch::Detail::stringify( m_comparator ); + } + + T const& m_comparator; + }; + + template + struct ContainsMatcher : MatcherBase, std::vector > { + + ContainsMatcher(std::vector const &comparator) : m_comparator( comparator ) {} + + bool match(std::vector const &v) const override { + // !TBD: see note in EqualsMatcher + if (m_comparator.size() > v.size()) + return false; + for (auto const& comparator : m_comparator) { + auto present = false; + for (const auto& el : v) { + if (el == comparator) { + present = true; + break; + } + } + if (!present) { + return false; + } + } + return true; + } + std::string describe() const override { + return "Contains: " + ::Catch::Detail::stringify( m_comparator ); + } + + std::vector const& m_comparator; + }; + + template + struct EqualsMatcher : MatcherBase, std::vector > { + + EqualsMatcher(std::vector const &comparator) : m_comparator( comparator ) {} + + bool match(std::vector const &v) const override { + // !TBD: This currently works if all elements can be compared using != + // - a more general approach would be via a compare template that defaults + // to using !=. but could be specialised for, e.g. std::vector etc + // - then just call that directly + if (m_comparator.size() != v.size()) + return false; + for (size_t i = 0; i < v.size(); ++i) + if (m_comparator[i] != v[i]) + return false; + return true; + } + std::string describe() const override { + return "Equals: " + ::Catch::Detail::stringify( m_comparator ); + } + std::vector const& m_comparator; + }; + + } // namespace Vector + + // The following functions create the actual matcher objects. + // This allows the types to be inferred + + template + Vector::ContainsMatcher Contains( std::vector const& comparator ) { + return Vector::ContainsMatcher( comparator ); + } + + template + Vector::ContainsElementMatcher VectorContains( T const& comparator ) { + return Vector::ContainsElementMatcher( comparator ); + } + + template + Vector::EqualsMatcher Equals( std::vector const& comparator ) { + return Vector::EqualsMatcher( comparator ); + } + +} // namespace Matchers +} // namespace Catch + +// end catch_matchers_vector.h +namespace Catch { + + template + class MatchExpr : public ITransientExpression { + ArgT const& m_arg; + MatcherT m_matcher; + StringRef m_matcherString; + bool m_result; + public: + MatchExpr( ArgT const& arg, MatcherT const& matcher, StringRef matcherString ) + : m_arg( arg ), + m_matcher( matcher ), + m_matcherString( matcherString ), + m_result( matcher.match( arg ) ) + {} + + auto isBinaryExpression() const -> bool override { return true; } + auto getResult() const -> bool override { return m_result; } + + void streamReconstructedExpression( std::ostream &os ) const override { + auto matcherAsString = m_matcher.toString(); + os << Catch::Detail::stringify( m_arg ) << ' '; + if( matcherAsString == Detail::unprintableString ) + os << m_matcherString; + else + os << matcherAsString; + } + }; + + using StringMatcher = Matchers::Impl::MatcherBase; + + void handleExceptionMatchExpr( AssertionHandler& handler, StringMatcher const& matcher, StringRef matcherString ); + + template + auto makeMatchExpr( ArgT const& arg, MatcherT const& matcher, StringRef matcherString ) -> MatchExpr { + return MatchExpr( arg, matcher, matcherString ); + } + +} // namespace Catch + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CHECK_THAT( macroName, matcher, resultDisposition, arg ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #arg ", " #matcher, resultDisposition ); \ + INTERNAL_CATCH_TRY( catchAssertionHandler ) { \ + catchAssertionHandler.handle( Catch::makeMatchExpr( arg, matcher, #matcher ) ); \ + } INTERNAL_CATCH_CATCH( catchAssertionHandler ) \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +/////////////////////////////////////////////////////////////////////////////// +#define INTERNAL_CATCH_THROWS_MATCHES( macroName, exceptionType, resultDisposition, matcher, ... ) \ + do { \ + Catch::AssertionHandler catchAssertionHandler( macroName, CATCH_INTERNAL_LINEINFO, #__VA_ARGS__ ", " #exceptionType ", " #matcher, resultDisposition ); \ + if( catchAssertionHandler.allowThrows() ) \ + try { \ + static_cast(__VA_ARGS__ ); \ + catchAssertionHandler.handle( Catch::ResultWas::DidntThrowException ); \ + } \ + catch( exceptionType const& ex ) { \ + catchAssertionHandler.handle( Catch::makeMatchExpr( ex, matcher, #matcher ) ); \ + } \ + catch( ... ) { \ + catchAssertionHandler.useActiveException(); \ + } \ + else \ + catchAssertionHandler.handle( Catch::ResultWas::Ok ); \ + INTERNAL_CATCH_REACT( catchAssertionHandler ) \ + } while( Catch::alwaysFalse() ) + +// end catch_capture_matchers.h +#endif + +// These files are included here so the single_include script doesn't put them +// in the conditionally compiled sections +// start catch_test_case_info.h + +#include +#include +#include + +#ifdef __clang__ +#pragma clang diagnostic push +#pragma clang diagnostic ignored "-Wpadded" +#endif + +namespace Catch { + + struct ITestInvoker; + + struct TestCaseInfo { + enum SpecialProperties{ + None = 0, + IsHidden = 1 << 1, + ShouldFail = 1 << 2, + MayFail = 1 << 3, + Throws = 1 << 4, + NonPortable = 1 << 5, + Benchmark = 1 << 6 + }; + + TestCaseInfo( std::string const& _name, + std::string const& _className, + std::string const& _description, + std::vector const& _tags, + SourceLineInfo const& _lineInfo ); + + friend void setTags( TestCaseInfo& testCaseInfo, std::vector tags ); + + bool isHidden() const; + bool throws() const; + bool okToFail() const; + bool expectedToFail() const; + + std::string tagsAsString() const; + + std::string name; + std::string className; + std::string description; + std::vector tags; + std::vector lcaseTags; + SourceLineInfo lineInfo; + SpecialProperties properties; + }; + + class TestCase : public TestCaseInfo { + public: + + TestCase( ITestInvoker* testCase, TestCaseInfo const& info ); + + TestCase withName( std::string const& _newName ) const; + + void invoke() const; + + TestCaseInfo const& getTestCaseInfo() const; + + bool operator == ( TestCase const& other ) const; + bool operator < ( TestCase const& other ) const; + + private: + std::shared_ptr test; + }; + + TestCase makeTestCase( ITestInvoker* testCase, + std::string const& className, + std::string const& name, + std::string const& description, + SourceLineInfo const& lineInfo ); +} + +#ifdef __clang__ +#pragma clang diagnostic pop +#endif + +// end catch_test_case_info.h +// start catch_interfaces_runner.h + +namespace Catch { + class TestCase; + + struct IRunner { + virtual ~IRunner(); + virtual bool aborting() const = 0; + }; +} + +// end catch_interfaces_runner.h + +#ifdef __OBJC__ +// start catch_objc.hpp + +#import + +#include + +// NB. Any general catch headers included here must be included +// in catch.hpp first to make sure they are included by the single +// header for non obj-usage + +/////////////////////////////////////////////////////////////////////////////// +// This protocol is really only here for (self) documenting purposes, since +// all its methods are optional. +@protocol OcFixture + +@optional + +-(void) setUp; +-(void) tearDown; + +@end + +namespace Catch { + + class OcMethod : public ITestInvoker { + + public: + OcMethod( Class cls, SEL sel ) : m_cls( cls ), m_sel( sel ) {} + + virtual void invoke() const { + id obj = [[m_cls alloc] init]; + + performOptionalSelector( obj, @selector(setUp) ); + performOptionalSelector( obj, m_sel ); + performOptionalSelector( obj, @selector(tearDown) ); + + arcSafeRelease( obj ); + } + private: + virtual ~OcMethod() {} + + Class m_cls; + SEL m_sel; + }; + + namespace Detail{ + + inline std::string getAnnotation( Class cls, + std::string const& annotationName, + std::string const& testCaseName ) { + NSString* selStr = [[NSString alloc] initWithFormat:@"Catch_%s_%s", annotationName.c_str(), testCaseName.c_str()]; + SEL sel = NSSelectorFromString( selStr ); + arcSafeRelease( selStr ); + id value = performOptionalSelector( cls, sel ); + if( value ) + return [(NSString*)value UTF8String]; + return ""; + } + } + + inline size_t registerTestMethods() { + size_t noTestMethods = 0; + int noClasses = objc_getClassList( nullptr, 0 ); + + Class* classes = (CATCH_UNSAFE_UNRETAINED Class *)malloc( sizeof(Class) * noClasses); + objc_getClassList( classes, noClasses ); + + for( int c = 0; c < noClasses; c++ ) { + Class cls = classes[c]; + { + u_int count; + Method* methods = class_copyMethodList( cls, &count ); + for( u_int m = 0; m < count ; m++ ) { + SEL selector = method_getName(methods[m]); + std::string methodName = sel_getName(selector); + if( startsWith( methodName, "Catch_TestCase_" ) ) { + std::string testCaseName = methodName.substr( 15 ); + std::string name = Detail::getAnnotation( cls, "Name", testCaseName ); + std::string desc = Detail::getAnnotation( cls, "Description", testCaseName ); + const char* className = class_getName( cls ); + + getMutableRegistryHub().registerTest( makeTestCase( new OcMethod( cls, selector ), className, name.c_str(), desc.c_str(), SourceLineInfo() ) ); + noTestMethods++; + } + } + free(methods); + } + } + return noTestMethods; + } + +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) + + namespace Matchers { + namespace Impl { + namespace NSStringMatchers { + + struct StringHolder : MatcherBase{ + StringHolder( NSString* substr ) : m_substr( [substr copy] ){} + StringHolder( StringHolder const& other ) : m_substr( [other.m_substr copy] ){} + StringHolder() { + arcSafeRelease( m_substr ); + } + + bool match( NSString* arg ) const override { + return false; + } + + NSString* m_substr; + }; + + struct Equals : StringHolder { + Equals( NSString* substr ) : StringHolder( substr ){} + + bool match( NSString* str ) const override { + return (str != nil || m_substr == nil ) && + [str isEqualToString:m_substr]; + } + + std::string describe() const override { + return "equals string: " + Catch::toString( m_substr ); + } + }; + + struct Contains : StringHolder { + Contains( NSString* substr ) : StringHolder( substr ){} + + bool match( NSString* str ) const { + return (str != nil || m_substr == nil ) && + [str rangeOfString:m_substr].location != NSNotFound; + } + + std::string describe() const override { + return "contains string: " + Catch::toString( m_substr ); + } + }; + + struct StartsWith : StringHolder { + StartsWith( NSString* substr ) : StringHolder( substr ){} + + bool match( NSString* str ) const override { + return (str != nil || m_substr == nil ) && + [str rangeOfString:m_substr].location == 0; + } + + std::string describe() const override { + return "starts with: " + Catch::toString( m_substr ); + } + }; + struct EndsWith : StringHolder { + EndsWith( NSString* substr ) : StringHolder( substr ){} + + bool match( NSString* str ) const override { + return (str != nil || m_substr == nil ) && + [str rangeOfString:m_substr].location == [str length] - [m_substr length]; + } + + std::string describe() const override { + return "ends with: " + Catch::toString( m_substr ); + } + }; + + } // namespace NSStringMatchers + } // namespace Impl + + inline Impl::NSStringMatchers::Equals + Equals( NSString* substr ){ return Impl::NSStringMatchers::Equals( substr ); } + + inline Impl::NSStringMatchers::Contains + Contains( NSString* substr ){ return Impl::NSStringMatchers::Contains( substr ); } + + inline Impl::NSStringMatchers::StartsWith + StartsWith( NSString* substr ){ return Impl::NSStringMatchers::StartsWith( substr ); } + + inline Impl::NSStringMatchers::EndsWith + EndsWith( NSString* substr ){ return Impl::NSStringMatchers::EndsWith( substr ); } + + } // namespace Matchers + + using namespace Matchers; + +#endif // CATCH_CONFIG_DISABLE_MATCHERS + +} // namespace Catch + +/////////////////////////////////////////////////////////////////////////////// +#define OC_TEST_CASE( name, desc )\ ++(NSString*) INTERNAL_CATCH_UNIQUE_NAME( Catch_Name_test ) \ +{\ +return @ name; \ +}\ ++(NSString*) INTERNAL_CATCH_UNIQUE_NAME( Catch_Description_test ) \ +{ \ +return @ desc; \ +} \ +-(void) INTERNAL_CATCH_UNIQUE_NAME( Catch_TestCase_test ) + +// end catch_objc.hpp +#endif + +#ifdef CATCH_CONFIG_EXTERNAL_INTERFACES +// start catch_external_interfaces.h +#ifndef TWOBLUECUBES_CATCH_EXTERNAL_INTERFACES_H +#define TWOBLUECUBES_CATCH_EXTERNAL_INTERFACES_H + +// start catch_reporter_bases.hpp + +// start catch_enforce.h + +#include +#include + +#define CATCH_PREPARE_EXCEPTION( type, msg ) \ + type( static_cast( std::ostringstream() << msg ).str() ) +#define CATCH_INTERNAL_ERROR( msg ) \ + throw CATCH_PREPARE_EXCEPTION( std::logic_error, CATCH_INTERNAL_LINEINFO << ": Internal Catch error: " << msg); +#define CATCH_ERROR( msg ) \ + throw CATCH_PREPARE_EXCEPTION( std::domain_error, msg ) +#define CATCH_ENFORCE( condition, msg ) \ + do{ if( !(condition) ) CATCH_ERROR( msg ); } while(false) + +// end catch_enforce.h +// start catch_interfaces_reporter.h + +// start catch_config.hpp + +// start catch_test_spec_parser.hpp + +#ifdef __clang__ +#pragma clang diagnostic push +#pragma clang diagnostic ignored "-Wpadded" +#endif + +// start catch_test_spec.hpp + +#ifdef __clang__ +#pragma clang diagnostic push +#pragma clang diagnostic ignored "-Wpadded" +#endif + +// start catch_wildcard_pattern.hpp + +#include + +namespace Catch +{ + class WildcardPattern { + enum WildcardPosition { + NoWildcard = 0, + WildcardAtStart = 1, + WildcardAtEnd = 2, + WildcardAtBothEnds = WildcardAtStart | WildcardAtEnd + }; + + public: + + WildcardPattern( std::string const& pattern, CaseSensitive::Choice caseSensitivity ); + virtual ~WildcardPattern() = default; + virtual bool matches( std::string const& str ) const; + + private: + std::string adjustCase( std::string const& str ) const; + CaseSensitive::Choice m_caseSensitivity; + WildcardPosition m_wildcard = NoWildcard; + std::string m_pattern; + }; +} + +// end catch_wildcard_pattern.hpp +#include +#include +#include + +namespace Catch { + + class TestSpec { + struct Pattern { + virtual ~Pattern() = default; + virtual bool matches( TestCaseInfo const& testCase ) const = 0; + }; + using PatternPtr = std::shared_ptr; + + class NamePattern : public Pattern { + public: + NamePattern( std::string const& name ); + virtual ~NamePattern() = default; + virtual bool matches( TestCaseInfo const& testCase ) const override; + private: + WildcardPattern m_wildcardPattern; + }; + + class TagPattern : public Pattern { + public: + TagPattern( std::string const& tag ); + virtual ~TagPattern() = default; + virtual bool matches( TestCaseInfo const& testCase ) const override; + private: + std::string m_tag; + }; + + class ExcludedPattern : public Pattern { + public: + ExcludedPattern( PatternPtr const& underlyingPattern ); + virtual ~ExcludedPattern() = default; + virtual bool matches( TestCaseInfo const& testCase ) const override; + private: + PatternPtr m_underlyingPattern; + }; + + struct Filter { + std::vector m_patterns; + + bool matches( TestCaseInfo const& testCase ) const; + }; + + public: + bool hasFilters() const; + bool matches( TestCaseInfo const& testCase ) const; + + private: + std::vector m_filters; + + friend class TestSpecParser; + }; +} + +#ifdef __clang__ +#pragma clang diagnostic pop +#endif + +// end catch_test_spec.hpp +// start catch_string_manip.h + +#include +#include + +namespace Catch { + + bool startsWith( std::string const& s, std::string const& prefix ); + bool startsWith( std::string const& s, char prefix ); + bool endsWith( std::string const& s, std::string const& suffix ); + bool endsWith( std::string const& s, char suffix ); + bool contains( std::string const& s, std::string const& infix ); + void toLowerInPlace( std::string& s ); + std::string toLower( std::string const& s ); + std::string trim( std::string const& str ); + bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis ); + + struct pluralise { + pluralise( std::size_t count, std::string const& label ); + + friend std::ostream& operator << ( std::ostream& os, pluralise const& pluraliser ); + + std::size_t m_count; + std::string m_label; + }; +} + +// end catch_string_manip.h +namespace Catch { + + class TestSpecParser { + enum Mode{ None, Name, QuotedName, Tag, EscapedName }; + Mode m_mode = None; + bool m_exclusion = false; + std::size_t m_start = std::string::npos, m_pos = 0; + std::string m_arg; + std::vector m_escapeChars; + TestSpec::Filter m_currentFilter; + TestSpec m_testSpec; + ITagAliasRegistry const* m_tagAliases = nullptr; + + public: + TestSpecParser( ITagAliasRegistry const& tagAliases ); + + TestSpecParser& parse( std::string const& arg ); + TestSpec testSpec(); + + private: + void visitChar( char c ); + void startNewMode( Mode mode, std::size_t start ); + void escape(); + std::string subString() const; + + template + void addPattern() { + std::string token = subString(); + for( size_t i = 0; i < m_escapeChars.size(); ++i ) + token = token.substr( 0, m_escapeChars[i]-m_start-i ) + token.substr( m_escapeChars[i]-m_start-i+1 ); + m_escapeChars.clear(); + if( startsWith( token, "exclude:" ) ) { + m_exclusion = true; + token = token.substr( 8 ); + } + if( !token.empty() ) { + TestSpec::PatternPtr pattern = std::make_shared( token ); + if( m_exclusion ) + pattern = std::make_shared( pattern ); + m_currentFilter.m_patterns.push_back( pattern ); + } + m_exclusion = false; + m_mode = None; + } + + void addFilter(); + }; + TestSpec parseTestSpec( std::string const& arg ); + +} // namespace Catch + +#ifdef __clang__ +#pragma clang diagnostic pop +#endif + +// end catch_test_spec_parser.hpp +// start catch_interfaces_config.h + +#include +#include +#include +#include + +namespace Catch { + + enum class Verbosity { + Quiet = 0, + Normal, + High + }; + + struct WarnAbout { enum What { + Nothing = 0x00, + NoAssertions = 0x01 + }; }; + + struct ShowDurations { enum OrNot { + DefaultForReporter, + Always, + Never + }; }; + struct RunTests { enum InWhatOrder { + InDeclarationOrder, + InLexicographicalOrder, + InRandomOrder + }; }; + struct UseColour { enum YesOrNo { + Auto, + Yes, + No + }; }; + struct WaitForKeypress { enum When { + Never, + BeforeStart = 1, + BeforeExit = 2, + BeforeStartAndExit = BeforeStart | BeforeExit + }; }; + + class TestSpec; + + struct IConfig : NonCopyable { + + virtual ~IConfig(); + + virtual bool allowThrows() const = 0; + virtual std::ostream& stream() const = 0; + virtual std::string name() const = 0; + virtual bool includeSuccessfulResults() const = 0; + virtual bool shouldDebugBreak() const = 0; + virtual bool warnAboutMissingAssertions() const = 0; + virtual int abortAfter() const = 0; + virtual bool showInvisibles() const = 0; + virtual ShowDurations::OrNot showDurations() const = 0; + virtual TestSpec const& testSpec() const = 0; + virtual RunTests::InWhatOrder runOrder() const = 0; + virtual unsigned int rngSeed() const = 0; + virtual int benchmarkResolutionMultiple() const = 0; + virtual UseColour::YesOrNo useColour() const = 0; + virtual std::vector const& getSectionsToRun() const = 0; + virtual Verbosity verbosity() const = 0; + }; + + using IConfigPtr = std::shared_ptr; +} + +// end catch_interfaces_config.h +// start catch_stream.h + +// start catch_streambuf.h + +#include + +namespace Catch { + + class StreamBufBase : public std::streambuf { + public: + virtual ~StreamBufBase() noexcept; + }; +} + +// end catch_streambuf.h +#include +#include +#include +#include + +namespace Catch { + + std::ostream& cout(); + std::ostream& cerr(); + std::ostream& clog(); + + struct IStream { + virtual ~IStream() noexcept; + virtual std::ostream& stream() const = 0; + }; + + class FileStream : public IStream { + mutable std::ofstream m_ofs; + public: + FileStream( std::string const& filename ); + ~FileStream() noexcept override; + public: // IStream + std::ostream& stream() const override; + }; + + class CoutStream : public IStream { + mutable std::ostream m_os; + public: + CoutStream(); + ~CoutStream() noexcept override; + + public: // IStream + std::ostream& stream() const override; + }; + + class DebugOutStream : public IStream { + std::unique_ptr m_streamBuf; + mutable std::ostream m_os; + public: + DebugOutStream(); + ~DebugOutStream() noexcept override; + + public: // IStream + std::ostream& stream() const override; + }; +} + +// end catch_stream.h +#include +#include +#include + +#ifndef CATCH_CONFIG_CONSOLE_WIDTH +#define CATCH_CONFIG_CONSOLE_WIDTH 80 +#endif + +namespace Catch { + + struct ConfigData { + bool listTests = false; + bool listTags = false; + bool listReporters = false; + bool listTestNamesOnly = false; + + bool showSuccessfulTests = false; + bool shouldDebugBreak = false; + bool noThrow = false; + bool showHelp = false; + bool showInvisibles = false; + bool filenamesAsTags = false; + bool libIdentify = false; + + int abortAfter = -1; + unsigned int rngSeed = 0; + int benchmarkResolutionMultiple = 100; + + Verbosity verbosity = Verbosity::Normal; + WarnAbout::What warnings = WarnAbout::Nothing; + ShowDurations::OrNot showDurations = ShowDurations::DefaultForReporter; + RunTests::InWhatOrder runOrder = RunTests::InDeclarationOrder; + UseColour::YesOrNo useColour = UseColour::Auto; + WaitForKeypress::When waitForKeypress = WaitForKeypress::Never; + + std::string outputFilename; + std::string name; + std::string processName; + + std::vector reporterNames; + std::vector testsOrTags; + std::vector sectionsToRun; + }; + + class Config : public IConfig { + virtual void dummy(); + public: + + Config() = default; + Config( ConfigData const& data ); + virtual ~Config() = default; + + std::string const& getFilename() const; + + bool listTests() const; + bool listTestNamesOnly() const; + bool listTags() const; + bool listReporters() const; + + std::string getProcessName() const; + + std::vector const& getReporterNames() const; + std::vector const& getSectionsToRun() const override; + + virtual TestSpec const& testSpec() const override; + + bool showHelp() const; + + // IConfig interface + bool allowThrows() const override; + std::ostream& stream() const override; + std::string name() const override; + bool includeSuccessfulResults() const override; + bool warnAboutMissingAssertions() const override; + ShowDurations::OrNot showDurations() const override; + RunTests::InWhatOrder runOrder() const override; + unsigned int rngSeed() const override; + int benchmarkResolutionMultiple() const override; + UseColour::YesOrNo useColour() const override; + bool shouldDebugBreak() const override; + int abortAfter() const override; + bool showInvisibles() const override; + Verbosity verbosity() const override; + + private: + + IStream const* openStream(); + ConfigData m_data; + + std::unique_ptr m_stream; + TestSpec m_testSpec; + }; + +} // end namespace Catch + +// end catch_config.hpp +// start catch_assertionresult.h + +#include + +namespace Catch { + + struct AssertionResultData + { + AssertionResultData() = delete; + + AssertionResultData( ResultWas::OfType _resultType, LazyExpression const& _lazyExpression ) + : resultType( _resultType ), + lazyExpression( _lazyExpression ) + {} + + ResultWas::OfType resultType = ResultWas::Unknown; + std::string message; + + LazyExpression lazyExpression; + + std::string reconstructExpression() const; + mutable std::string reconstructedExpression; + }; + + class AssertionResult { + public: + AssertionResult() = delete; + AssertionResult( AssertionInfo const& info, AssertionResultData const& data ); + + bool isOk() const; + bool succeeded() const; + ResultWas::OfType getResultType() const; + bool hasExpression() const; + bool hasMessage() const; + std::string getExpression() const; + std::string getExpressionInMacro() const; + bool hasExpandedExpression() const; + std::string getExpandedExpression() const; + std::string getMessage() const; + SourceLineInfo getSourceInfo() const; + std::string getTestMacroName() const; + + //protected: + AssertionInfo m_info; + AssertionResultData m_resultData; + }; + +} // end namespace Catch + +// end catch_assertionresult.h +// start catch_option.hpp + +namespace Catch { + + // An optional type + template + class Option { + public: + Option() : nullableValue( nullptr ) {} + Option( T const& _value ) + : nullableValue( new( storage ) T( _value ) ) + {} + Option( Option const& _other ) + : nullableValue( _other ? new( storage ) T( *_other ) : nullptr ) + {} + + ~Option() { + reset(); + } + + Option& operator= ( Option const& _other ) { + if( &_other != this ) { + reset(); + if( _other ) + nullableValue = new( storage ) T( *_other ); + } + return *this; + } + Option& operator = ( T const& _value ) { + reset(); + nullableValue = new( storage ) T( _value ); + return *this; + } + + void reset() { + if( nullableValue ) + nullableValue->~T(); + nullableValue = nullptr; + } + + T& operator*() { return *nullableValue; } + T const& operator*() const { return *nullableValue; } + T* operator->() { return nullableValue; } + const T* operator->() const { return nullableValue; } + + T valueOr( T const& defaultValue ) const { + return nullableValue ? *nullableValue : defaultValue; + } + + bool some() const { return nullableValue != nullptr; } + bool none() const { return nullableValue == nullptr; } + + bool operator !() const { return nullableValue == nullptr; } + explicit operator bool() const { + return some(); + } + + private: + T *nullableValue; + alignas(alignof(T)) char storage[sizeof(T)]; + }; + +} // end namespace Catch + +// end catch_option.hpp +#include +#include +#include +#include +#include + +namespace Catch { + + struct ReporterConfig { + explicit ReporterConfig( IConfigPtr const& _fullConfig ); + + ReporterConfig( IConfigPtr const& _fullConfig, std::ostream& _stream ); + + std::ostream& stream() const; + IConfigPtr fullConfig() const; + + private: + std::ostream* m_stream; + IConfigPtr m_fullConfig; + }; + + struct ReporterPreferences { + bool shouldRedirectStdOut = false; + }; + + template + struct LazyStat : Option { + LazyStat& operator=( T const& _value ) { + Option::operator=( _value ); + used = false; + return *this; + } + void reset() { + Option::reset(); + used = false; + } + bool used = false; + }; + + struct TestRunInfo { + TestRunInfo( std::string const& _name ); + std::string name; + }; + struct GroupInfo { + GroupInfo( std::string const& _name, + std::size_t _groupIndex, + std::size_t _groupsCount ); + + std::string name; + std::size_t groupIndex; + std::size_t groupsCounts; + }; + + struct AssertionStats { + AssertionStats( AssertionResult const& _assertionResult, + std::vector const& _infoMessages, + Totals const& _totals ); + + AssertionStats( AssertionStats const& ) = default; + AssertionStats( AssertionStats && ) = default; + AssertionStats& operator = ( AssertionStats const& ) = default; + AssertionStats& operator = ( AssertionStats && ) = default; + virtual ~AssertionStats() = default; + + AssertionResult assertionResult; + std::vector infoMessages; + Totals totals; + }; + + struct SectionStats { + SectionStats( SectionInfo const& _sectionInfo, + Counts const& _assertions, + double _durationInSeconds, + bool _missingAssertions ); + SectionStats( SectionStats const& ) = default; + SectionStats( SectionStats && ) = default; + SectionStats& operator = ( SectionStats const& ) = default; + SectionStats& operator = ( SectionStats && ) = default; + virtual ~SectionStats() = default; + + SectionInfo sectionInfo; + Counts assertions; + double durationInSeconds; + bool missingAssertions; + }; + + struct TestCaseStats { + TestCaseStats( TestCaseInfo const& _testInfo, + Totals const& _totals, + std::string const& _stdOut, + std::string const& _stdErr, + bool _aborting ); + + TestCaseStats( TestCaseStats const& ) = default; + TestCaseStats( TestCaseStats && ) = default; + TestCaseStats& operator = ( TestCaseStats const& ) = default; + TestCaseStats& operator = ( TestCaseStats && ) = default; + virtual ~TestCaseStats() = default; + + TestCaseInfo testInfo; + Totals totals; + std::string stdOut; + std::string stdErr; + bool aborting; + }; + + struct TestGroupStats { + TestGroupStats( GroupInfo const& _groupInfo, + Totals const& _totals, + bool _aborting ); + TestGroupStats( GroupInfo const& _groupInfo ); + + TestGroupStats( TestGroupStats const& ) = default; + TestGroupStats( TestGroupStats && ) = default; + TestGroupStats& operator = ( TestGroupStats const& ) = default; + TestGroupStats& operator = ( TestGroupStats && ) = default; + virtual ~TestGroupStats() = default; + + GroupInfo groupInfo; + Totals totals; + bool aborting; + }; + + struct TestRunStats { + TestRunStats( TestRunInfo const& _runInfo, + Totals const& _totals, + bool _aborting ); + + TestRunStats( TestRunStats const& ) = default; + TestRunStats( TestRunStats && ) = default; + TestRunStats& operator = ( TestRunStats const& ) = default; + TestRunStats& operator = ( TestRunStats && ) = default; + virtual ~TestRunStats() = default; + + TestRunInfo runInfo; + Totals totals; + bool aborting; + }; + + struct BenchmarkInfo { + std::string name; + }; + struct BenchmarkStats { + BenchmarkInfo info; + size_t iterations; + uint64_t elapsedTimeInNanoseconds; + }; + class MultipleReporters; + + struct IStreamingReporter { + virtual ~IStreamingReporter() = default; + + // Implementing class must also provide the following static methods: + // static std::string getDescription(); + // static std::set getSupportedVerbosities() + + virtual ReporterPreferences getPreferences() const = 0; + + virtual void noMatchingTestCases( std::string const& spec ) = 0; + + virtual void testRunStarting( TestRunInfo const& testRunInfo ) = 0; + virtual void testGroupStarting( GroupInfo const& groupInfo ) = 0; + + virtual void testCaseStarting( TestCaseInfo const& testInfo ) = 0; + virtual void sectionStarting( SectionInfo const& sectionInfo ) = 0; + + // *** experimental *** + virtual void benchmarkStarting( BenchmarkInfo const& ) {} + + virtual void assertionStarting( AssertionInfo const& assertionInfo ) = 0; + + // The return value indicates if the messages buffer should be cleared: + virtual bool assertionEnded( AssertionStats const& assertionStats ) = 0; + + // *** experimental *** + virtual void benchmarkEnded( BenchmarkStats const& ) {} + + virtual void sectionEnded( SectionStats const& sectionStats ) = 0; + virtual void testCaseEnded( TestCaseStats const& testCaseStats ) = 0; + virtual void testGroupEnded( TestGroupStats const& testGroupStats ) = 0; + virtual void testRunEnded( TestRunStats const& testRunStats ) = 0; + + virtual void skipTest( TestCaseInfo const& testInfo ) = 0; + + virtual bool isMulti() const; + }; + using IStreamingReporterPtr = std::unique_ptr; + + struct IReporterFactory { + virtual ~IReporterFactory() = default; + virtual IStreamingReporterPtr create( ReporterConfig const& config ) const = 0; + virtual std::string getDescription() const = 0; + }; + using IReporterFactoryPtr = std::shared_ptr; + + struct IReporterRegistry { + using FactoryMap = std::map; + using Listeners = std::vector; + + virtual ~IReporterRegistry() = default; + virtual IStreamingReporterPtr create( std::string const& name, IConfigPtr const& config ) const = 0; + virtual FactoryMap const& getFactories() const = 0; + virtual Listeners const& getListeners() const = 0; + }; + + void addReporter( IStreamingReporterPtr& existingReporter, IStreamingReporterPtr&& additionalReporter ); + +} // end namespace Catch + +// end catch_interfaces_reporter.h +#include +#include +#include +#include +#include +#include + +namespace Catch { + void prepareExpandedExpression(AssertionResult& result); + + // Returns double formatted as %.3f (format expected on output) + std::string getFormattedDuration( double duration ); + + template + struct StreamingReporterBase : IStreamingReporter { + + StreamingReporterBase( ReporterConfig const& _config ) + : m_config( _config.fullConfig() ), + stream( _config.stream() ) + { + m_reporterPrefs.shouldRedirectStdOut = false; + CATCH_ENFORCE( DerivedT::getSupportedVerbosities().count( m_config->verbosity() ), "Verbosity level not supported by this reporter" ); + } + + ReporterPreferences getPreferences() const override { + return m_reporterPrefs; + } + + static std::set getSupportedVerbosities() { + return { Verbosity::Normal }; + } + + ~StreamingReporterBase() override = default; + + void noMatchingTestCases(std::string const&) override {} + + void testRunStarting(TestRunInfo const& _testRunInfo) override { + currentTestRunInfo = _testRunInfo; + } + void testGroupStarting(GroupInfo const& _groupInfo) override { + currentGroupInfo = _groupInfo; + } + + void testCaseStarting(TestCaseInfo const& _testInfo) override { + currentTestCaseInfo = _testInfo; + } + void sectionStarting(SectionInfo const& _sectionInfo) override { + m_sectionStack.push_back(_sectionInfo); + } + + void sectionEnded(SectionStats const& /* _sectionStats */) override { + m_sectionStack.pop_back(); + } + void testCaseEnded(TestCaseStats const& /* _testCaseStats */) override { + currentTestCaseInfo.reset(); + } + void testGroupEnded(TestGroupStats const& /* _testGroupStats */) override { + currentGroupInfo.reset(); + } + void testRunEnded(TestRunStats const& /* _testRunStats */) override { + currentTestCaseInfo.reset(); + currentGroupInfo.reset(); + currentTestRunInfo.reset(); + } + + void skipTest(TestCaseInfo const&) override { + // Don't do anything with this by default. + // It can optionally be overridden in the derived class. + } + + IConfigPtr m_config; + std::ostream& stream; + + LazyStat currentTestRunInfo; + LazyStat currentGroupInfo; + LazyStat currentTestCaseInfo; + + std::vector m_sectionStack; + ReporterPreferences m_reporterPrefs; + }; + + template + struct CumulativeReporterBase : IStreamingReporter { + template + struct Node { + explicit Node( T const& _value ) : value( _value ) {} + virtual ~Node() {} + + using ChildNodes = std::vector>; + T value; + ChildNodes children; + }; + struct SectionNode { + explicit SectionNode(SectionStats const& _stats) : stats(_stats) {} + virtual ~SectionNode() = default; + + bool operator == (SectionNode const& other) const { + return stats.sectionInfo.lineInfo == other.stats.sectionInfo.lineInfo; + } + bool operator == (std::shared_ptr const& other) const { + return operator==(*other); + } + + SectionStats stats; + using ChildSections = std::vector>; + using Assertions = std::vector; + ChildSections childSections; + Assertions assertions; + std::string stdOut; + std::string stdErr; + }; + + struct BySectionInfo { + BySectionInfo( SectionInfo const& other ) : m_other( other ) {} + BySectionInfo( BySectionInfo const& other ) : m_other( other.m_other ) {} + bool operator() (std::shared_ptr const& node) const { + return ((node->stats.sectionInfo.name == m_other.name) && + (node->stats.sectionInfo.lineInfo == m_other.lineInfo)); + } + void operator=(BySectionInfo const&) = delete; + + private: + SectionInfo const& m_other; + }; + + using TestCaseNode = Node; + using TestGroupNode = Node; + using TestRunNode = Node; + + CumulativeReporterBase( ReporterConfig const& _config ) + : m_config( _config.fullConfig() ), + stream( _config.stream() ) + { + m_reporterPrefs.shouldRedirectStdOut = false; + CATCH_ENFORCE( DerivedT::getSupportedVerbosities().count( m_config->verbosity() ), "Verbosity level not supported by this reporter" ); + } + ~CumulativeReporterBase() override = default; + + ReporterPreferences getPreferences() const override { + return m_reporterPrefs; + } + + static std::set getSupportedVerbosities() { + return { Verbosity::Normal }; + } + + void testRunStarting( TestRunInfo const& ) override {} + void testGroupStarting( GroupInfo const& ) override {} + + void testCaseStarting( TestCaseInfo const& ) override {} + + void sectionStarting( SectionInfo const& sectionInfo ) override { + SectionStats incompleteStats( sectionInfo, Counts(), 0, false ); + std::shared_ptr node; + if( m_sectionStack.empty() ) { + if( !m_rootSection ) + m_rootSection = std::make_shared( incompleteStats ); + node = m_rootSection; + } + else { + SectionNode& parentNode = *m_sectionStack.back(); + typename SectionNode::ChildSections::const_iterator it = + std::find_if( parentNode.childSections.begin(), + parentNode.childSections.end(), + BySectionInfo( sectionInfo ) ); + if( it == parentNode.childSections.end() ) { + node = std::make_shared( incompleteStats ); + parentNode.childSections.push_back( node ); + } + else + node = *it; + } + m_sectionStack.push_back( node ); + m_deepestSection = std::move(node); + } + + void assertionStarting(AssertionInfo const&) override {} + + bool assertionEnded(AssertionStats const& assertionStats) override { + assert(!m_sectionStack.empty()); + // AssertionResult holds a pointer to a temporary DecomposedExpression, + // which getExpandedExpression() calls to build the expression string. + // Our section stack copy of the assertionResult will likely outlive the + // temporary, so it must be expanded or discarded now to avoid calling + // a destroyed object later. + prepareExpandedExpression(const_cast( assertionStats.assertionResult ) ); + SectionNode& sectionNode = *m_sectionStack.back(); + sectionNode.assertions.push_back(assertionStats); + return true; + } + void sectionEnded(SectionStats const& sectionStats) override { + assert(!m_sectionStack.empty()); + SectionNode& node = *m_sectionStack.back(); + node.stats = sectionStats; + m_sectionStack.pop_back(); + } + void testCaseEnded(TestCaseStats const& testCaseStats) override { + auto node = std::make_shared(testCaseStats); + assert(m_sectionStack.size() == 0); + node->children.push_back(m_rootSection); + m_testCases.push_back(node); + m_rootSection.reset(); + + assert(m_deepestSection); + m_deepestSection->stdOut = testCaseStats.stdOut; + m_deepestSection->stdErr = testCaseStats.stdErr; + } + void testGroupEnded(TestGroupStats const& testGroupStats) override { + auto node = std::make_shared(testGroupStats); + node->children.swap(m_testCases); + m_testGroups.push_back(node); + } + void testRunEnded(TestRunStats const& testRunStats) override { + auto node = std::make_shared(testRunStats); + node->children.swap(m_testGroups); + m_testRuns.push_back(node); + testRunEndedCumulative(); + } + virtual void testRunEndedCumulative() = 0; + + void skipTest(TestCaseInfo const&) override {} + + IConfigPtr m_config; + std::ostream& stream; + std::vector m_assertions; + std::vector>> m_sections; + std::vector> m_testCases; + std::vector> m_testGroups; + + std::vector> m_testRuns; + + std::shared_ptr m_rootSection; + std::shared_ptr m_deepestSection; + std::vector> m_sectionStack; + ReporterPreferences m_reporterPrefs; + }; + + template + char const* getLineOfChars() { + static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0}; + if( !*line ) { + std::memset( line, C, CATCH_CONFIG_CONSOLE_WIDTH-1 ); + line[CATCH_CONFIG_CONSOLE_WIDTH-1] = 0; + } + return line; + } + + struct TestEventListenerBase : StreamingReporterBase { + TestEventListenerBase( ReporterConfig const& _config ); + + void assertionStarting(AssertionInfo const&) override; + bool assertionEnded(AssertionStats const&) override; + }; + +} // end namespace Catch + +// end catch_reporter_bases.hpp +// start catch_reporter_registrars.hpp + + +namespace Catch { + + template + class ReporterRegistrar { + + class ReporterFactory : public IReporterFactory { + + virtual IStreamingReporterPtr create( ReporterConfig const& config ) const override { + return std::unique_ptr( new T( config ) ); + } + + virtual std::string getDescription() const override { + return T::getDescription(); + } + }; + + public: + + ReporterRegistrar( std::string const& name ) { + getMutableRegistryHub().registerReporter( name, std::make_shared() ); + } + }; + + template + class ListenerRegistrar { + + class ListenerFactory : public IReporterFactory { + + virtual IStreamingReporterPtr create( ReporterConfig const& config ) const override { + return std::unique_ptr( new T( config ) ); + } + virtual std::string getDescription() const override { + return std::string(); + } + }; + + public: + + ListenerRegistrar() { + getMutableRegistryHub().registerListener( std::make_shared() ); + } + }; +} + +#define CATCH_REGISTER_REPORTER( name, reporterType ) \ + namespace{ Catch::ReporterRegistrar catch_internal_RegistrarFor##reporterType( name ); } + +#define CATCH_REGISTER_LISTENER( listenerType ) \ + namespace{ Catch::ListenerRegistrar catch_internal_RegistrarFor##listenerType; } + +// end catch_reporter_registrars.hpp +#endif // TWOBLUECUBES_CATCH_EXTERNAL_INTERFACES_H +// end catch_external_interfaces.h +#endif + +#ifdef CATCH_IMPL +// start catch_impl.hpp + +// Collect all the implementation files together here +// These are the equivalent of what would usually be cpp files + +#ifdef __clang__ +#pragma clang diagnostic push +#pragma clang diagnostic ignored "-Wweak-vtables" +#endif + +// start catch_notimplemented_exception.h + +#include + +namespace Catch { + + class NotImplementedException : public std::exception + { + public: + NotImplementedException( SourceLineInfo const& lineInfo ); + + virtual ~NotImplementedException() noexcept = default; + + virtual const char* what() const noexcept override; + + private: + std::string m_what; + }; + +} // end namespace Catch + +/////////////////////////////////////////////////////////////////////////////// +#define CATCH_NOT_IMPLEMENTED throw Catch::NotImplementedException( CATCH_INTERNAL_LINEINFO ) + +// end catch_notimplemented_exception.h +// Temporary hack to fix separately provided reporters +// + +// start catch_leak_detector.h + +namespace Catch { + + struct LeakDetector { + LeakDetector(); + }; + +} +// end catch_leak_detector.h +// start catch_session.hpp + +// start catch_commandline.hpp + +// start catch_clara.h + +// Use Catch's value for console width (store Clara's off to the side, if present) +#ifdef CLARA_CONFIG_CONSOLE_WIDTH +#define CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH +#undef CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH +#endif +#define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH CATCH_CONFIG_CONSOLE_WIDTH-1 + +// start clara.hpp +// v1.0 +// See https://github.com/philsquared/Clara + + +#ifndef CATCH_CLARA_CONFIG_CONSOLE_WIDTH +#define CATCH_CLARA_CONFIG_CONSOLE_WIDTH 80 +#endif + +// ----------- #included from clara_textflow.hpp ----------- + +// TextFlowCpp +// +// A single-header library for wrapping and laying out basic text, by Phil Nash +// +// This work is licensed under the BSD 2-Clause license. +// See the accompanying LICENSE file, or the one at https://opensource.org/licenses/BSD-2-Clause +// +// This project is hosted at https://github.com/philsquared/textflowcpp + + +#include +#include +#include +#include + +#ifndef CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH +#define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH 80 +#endif + +namespace Catch { namespace clara { namespace TextFlow { + + inline auto isWhitespace( char c ) -> bool { + static std::string chars = " \t\n\r"; + return chars.find( c ) != std::string::npos; + } + inline auto isBreakableBefore( char c ) -> bool { + static std::string chars = "[({<|"; + return chars.find( c ) != std::string::npos; + } + inline auto isBreakableAfter( char c ) -> bool { + static std::string chars = "])}>.,:;*+-=&/\\"; + return chars.find( c ) != std::string::npos; + } + + class Columns; + + class Column { + std::vector m_strings; + size_t m_width = CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH; + size_t m_indent = 0; + size_t m_initialIndent = std::string::npos; + + public: + class iterator { + friend Column; + + Column const& m_column; + size_t m_stringIndex = 0; + size_t m_pos = 0; + + size_t m_len = 0; + size_t m_end = 0; + bool m_suffix = false; + + iterator( Column const& column, size_t stringIndex ) + : m_column( column ), + m_stringIndex( stringIndex ) + {} + + auto line() const -> std::string const& { return m_column.m_strings[m_stringIndex]; } + + auto isBoundary( size_t at ) const -> bool { + assert( at > 0 ); + assert( at <= line().size() ); + + return at == line().size() || + ( isWhitespace( line()[at] ) && !isWhitespace( line()[at-1] ) ) || + isBreakableBefore( line()[at] ) || + isBreakableAfter( line()[at-1] ); + } + + void calcLength() { + assert( m_stringIndex < m_column.m_strings.size() ); + + m_suffix = false; + auto width = m_column.m_width-indent(); + m_end = m_pos; + while( m_end < line().size() && line()[m_end] != '\n' ) + ++m_end; + + if( m_end < m_pos + width ) { + m_len = m_end - m_pos; + } + else { + size_t len = width; + while (len > 0 && !isBoundary(m_pos + len)) + --len; + while (len > 0 && isWhitespace( line()[m_pos + len - 1] )) + --len; + + if (len > 0) { + m_len = len; + } else { + m_suffix = true; + m_len = width - 1; + } + } + } + + auto indent() const -> size_t { + auto initial = m_pos == 0 && m_stringIndex == 0 ? m_column.m_initialIndent : std::string::npos; + return initial == std::string::npos ? m_column.m_indent : initial; + } + + auto addIndentAndSuffix(std::string const &plain) const -> std::string { + return std::string( indent(), ' ' ) + (m_suffix ? plain + "-" : plain); + } + + public: + explicit iterator( Column const& column ) : m_column( column ) { + assert( m_column.m_width > m_column.m_indent ); + assert( m_column.m_initialIndent == std::string::npos || m_column.m_width > m_column.m_initialIndent ); + calcLength(); + if( m_len == 0 ) + m_stringIndex++; // Empty string + } + + auto operator *() const -> std::string { + assert( m_stringIndex < m_column.m_strings.size() ); + assert( m_pos < m_end ); + if( m_pos + m_column.m_width < m_end ) + return addIndentAndSuffix(line().substr(m_pos, m_len)); + else + return addIndentAndSuffix(line().substr(m_pos, m_end - m_pos)); + } + + auto operator ++() -> iterator& { + m_pos += m_len; + if( m_pos < line().size() && line()[m_pos] == '\n' ) + m_pos += 1; + else + while( m_pos < line().size() && isWhitespace( line()[m_pos] ) ) + ++m_pos; + + if( m_pos == line().size() ) { + m_pos = 0; + ++m_stringIndex; + } + if( m_stringIndex < m_column.m_strings.size() ) + calcLength(); + return *this; + } + auto operator ++(int) -> iterator { + iterator prev( *this ); + operator++(); + return prev; + } + + auto operator ==( iterator const& other ) const -> bool { + return + m_pos == other.m_pos && + m_stringIndex == other.m_stringIndex && + &m_column == &other.m_column; + } + auto operator !=( iterator const& other ) const -> bool { + return !operator==( other ); + } + }; + using const_iterator = iterator; + + explicit Column( std::string const& text ) { m_strings.push_back( text ); } + + auto width( size_t newWidth ) -> Column& { + assert( newWidth > 0 ); + m_width = newWidth; + return *this; + } + auto indent( size_t newIndent ) -> Column& { + m_indent = newIndent; + return *this; + } + auto initialIndent( size_t newIndent ) -> Column& { + m_initialIndent = newIndent; + return *this; + } + + auto width() const -> size_t { return m_width; } + auto begin() const -> iterator { return iterator( *this ); } + auto end() const -> iterator { return { *this, m_strings.size() }; } + + inline friend std::ostream& operator << ( std::ostream& os, Column const& col ) { + bool first = true; + for( auto line : col ) { + if( first ) + first = false; + else + os << "\n"; + os << line; + } + return os; + } + + auto operator + ( Column const& other ) -> Columns; + + auto toString() const -> std::string { + std::ostringstream oss; + oss << *this; + return oss.str(); + } + }; + + class Spacer : public Column { + + public: + explicit Spacer( size_t spaceWidth ) : Column( "" ) { + width( spaceWidth ); + } + }; + + class Columns { + std::vector m_columns; + + public: + + class iterator { + friend Columns; + struct EndTag {}; + + std::vector const& m_columns; + std::vector m_iterators; + size_t m_activeIterators; + + iterator( Columns const& columns, EndTag ) + : m_columns( columns.m_columns ), + m_activeIterators( 0 ) + { + m_iterators.reserve( m_columns.size() ); + + for( auto const& col : m_columns ) + m_iterators.push_back( col.end() ); + } + + public: + explicit iterator( Columns const& columns ) + : m_columns( columns.m_columns ), + m_activeIterators( m_columns.size() ) + { + m_iterators.reserve( m_columns.size() ); + + for( auto const& col : m_columns ) + m_iterators.push_back( col.begin() ); + } + + auto operator ==( iterator const& other ) const -> bool { + return m_iterators == other.m_iterators; + } + auto operator !=( iterator const& other ) const -> bool { + return m_iterators != other.m_iterators; + } + auto operator *() const -> std::string { + std::string row, padding; + + for( size_t i = 0; i < m_columns.size(); ++i ) { + auto width = m_columns[i].width(); + if( m_iterators[i] != m_columns[i].end() ) { + std::string col = *m_iterators[i]; + row += padding + col; + if( col.size() < width ) + padding = std::string( width - col.size(), ' ' ); + else + padding = ""; + } + else { + padding += std::string( width, ' ' ); + } + } + return row; + } + auto operator ++() -> iterator& { + for( size_t i = 0; i < m_columns.size(); ++i ) { + if (m_iterators[i] != m_columns[i].end()) + ++m_iterators[i]; + } + return *this; + } + auto operator ++(int) -> iterator { + iterator prev( *this ); + operator++(); + return prev; + } + }; + using const_iterator = iterator; + + auto begin() const -> iterator { return iterator( *this ); } + auto end() const -> iterator { return { *this, iterator::EndTag() }; } + + auto operator += ( Column const& col ) -> Columns& { + m_columns.push_back( col ); + return *this; + } + auto operator + ( Column const& col ) -> Columns { + Columns combined = *this; + combined += col; + return combined; + } + + inline friend std::ostream& operator << ( std::ostream& os, Columns const& cols ) { + + bool first = true; + for( auto line : cols ) { + if( first ) + first = false; + else + os << "\n"; + os << line; + } + return os; + } + + auto toString() const -> std::string { + std::ostringstream oss; + oss << *this; + return oss.str(); + } + }; + + inline auto Column::operator + ( Column const& other ) -> Columns { + Columns cols; + cols += *this; + cols += other; + return cols; + } +}}} // namespace Catch::clara::TextFlow + +// ----------- end of #include from clara_textflow.hpp ----------- +// ........... back in clara.hpp + +#include +#include +#include + +#if !defined(CLARA_PLATFORM_WINDOWS) && ( defined(WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_MSC_VER) ) +#define CLARA_PLATFORM_WINDOWS + +#endif + +namespace Catch { namespace clara { +namespace detail { + + // Traits for extracting arg and return type of lambdas (for single argument lambdas) + template + struct UnaryLambdaTraits : UnaryLambdaTraits {}; + + template + struct UnaryLambdaTraits { + static const bool isValid = false; + }; + + template + struct UnaryLambdaTraits { + static const bool isValid = true; + using ArgType = typename std::remove_const::type>::type;; + using ReturnType = ReturnT; + }; + + class TokenStream; + + // Transport for raw args (copied from main args, or supplied via init list for testing) + class Args { + friend TokenStream; + std::string m_exeName; + std::vector m_args; + + public: + Args(int argc, char *argv[]) { + m_exeName = argv[0]; + for (int i = 1; i < argc; ++i) + m_args.push_back(argv[i]); + } + + Args(std::initializer_list args) + : m_exeName( *args.begin() ), + m_args( args.begin()+1, args.end() ) + {} + + auto exeName() const -> std::string { + return m_exeName; + } + }; + + // Wraps a token coming from a token stream. These may not directly correspond to strings as a single string + // may encode an option + its argument if the : or = form is used + enum class TokenType { + Option, Argument + }; + struct Token { + TokenType type; + std::string token; + }; + + // Abstracts iterators into args as a stream of tokens, with option arguments uniformly handled + class TokenStream { + using Iterator = std::vector::const_iterator; + Iterator it; + Iterator itEnd; + std::vector m_tokenBuffer; + + void loadBuffer() { + m_tokenBuffer.resize(0); + + // Skip any empty strings + while (it != itEnd && it->empty()) + ++it; + + if (it != itEnd) { + auto const &next = *it; + if (next[0] == '-' || next[0] == '/') { + auto delimiterPos = next.find_first_of(" :="); + if (delimiterPos != std::string::npos) { + m_tokenBuffer.push_back({TokenType::Option, next.substr(0, delimiterPos)}); + m_tokenBuffer.push_back({TokenType::Argument, next.substr(delimiterPos + 1)}); + } else { + if (next[1] != '-' && next.size() > 2) { + std::string opt = "- "; + for (size_t i = 1; i < next.size(); ++i) { + opt[1] = next[i]; + m_tokenBuffer.push_back({TokenType::Option, opt}); + } + } else { + m_tokenBuffer.push_back({TokenType::Option, next}); + } + } + } else { + m_tokenBuffer.push_back({TokenType::Argument, next}); + } + } + } + + public: + explicit TokenStream(Args const &args) : TokenStream(args.m_args.begin(), args.m_args.end()) {} + + TokenStream(Iterator it, Iterator itEnd) : it(it), itEnd(itEnd) { + loadBuffer(); + } + + explicit operator bool() const { + return !m_tokenBuffer.empty() || it != itEnd; + } + + auto count() const -> size_t { return m_tokenBuffer.size() + (itEnd - it); } + + auto operator*() const -> Token { + assert(!m_tokenBuffer.empty()); + return m_tokenBuffer.front(); + } + + auto operator->() const -> Token const * { + assert(!m_tokenBuffer.empty()); + return &m_tokenBuffer.front(); + } + + auto operator++() -> TokenStream & { + if (m_tokenBuffer.size() >= 2) { + m_tokenBuffer.erase(m_tokenBuffer.begin()); + } else { + if (it != itEnd) + ++it; + loadBuffer(); + } + return *this; + } + }; + + class ResultBase { + public: + enum Type { + Ok, LogicError, RuntimeError + }; + + protected: + ResultBase(Type type) : m_type(type) {} + virtual ~ResultBase() = default; + + virtual void enforceOk() const = 0; + + Type m_type; + }; + + template + class ResultValueBase : public ResultBase { + public: + auto value() const -> T const & { + enforceOk(); + return m_value; + } + + protected: + ResultValueBase(Type type) : ResultBase(type) {} + + ResultValueBase(ResultValueBase const &other) : ResultBase(other) { + if (m_type == ResultBase::Ok) + new(&m_value) T(other.m_value); + } + + ResultValueBase(Type, T const &value) : ResultBase(Ok) { + new(&m_value) T(value); + } + + auto operator=(ResultValueBase const &other) -> ResultValueBase & { + if (m_type == ResultBase::Ok) + m_value.~T(); + ResultBase::operator=(other); + if (m_type == ResultBase::Ok) + new(&m_value) T(other.m_value); + return *this; + } + + ~ResultValueBase() { + if (m_type == Ok) + m_value.~T(); + } + + union { + T m_value; + }; + }; + + template<> + class ResultValueBase : public ResultBase { + protected: + using ResultBase::ResultBase; + }; + + template + class BasicResult : public ResultValueBase { + public: + template + explicit BasicResult(BasicResult const &other) + : ResultValueBase(other.type()), + m_errorMessage(other.errorMessage()) { + assert(type() != ResultBase::Ok); + } + + static auto ok() -> BasicResult { return {ResultBase::Ok}; } + + template + static auto ok(U const &value) -> BasicResult { return {ResultBase::Ok, value}; } + + static auto logicError(std::string const &message) -> BasicResult { return {ResultBase::LogicError, message}; } + + static auto runtimeError(std::string const &message) -> BasicResult { + return {ResultBase::RuntimeError, message}; + } + + explicit operator bool() const { return m_type == ResultBase::Ok; } + + auto type() const -> ResultBase::Type { return m_type; } + + auto errorMessage() const -> std::string { return m_errorMessage; } + + protected: + virtual void enforceOk() const { + // !TBD: If no exceptions, std::terminate here or something + switch (m_type) { + case ResultBase::LogicError: + throw std::logic_error(m_errorMessage); + case ResultBase::RuntimeError: + throw std::runtime_error(m_errorMessage); + case ResultBase::Ok: + break; + } + } + + std::string m_errorMessage; // Only populated if resultType is an error + + BasicResult(ResultBase::Type type, std::string const &message) + : ResultValueBase(type), + m_errorMessage(message) { + assert(m_type != ResultBase::Ok); + } + + using ResultValueBase::ResultValueBase; + using ResultBase::m_type; + }; + + enum class ParseResultType { + Matched, NoMatch, ShortCircuitAll, ShortCircuitSame + }; + + class ParseState { + public: + + ParseState(ParseResultType type, TokenStream const &remainingTokens) + : m_type(type), + m_remainingTokens(remainingTokens) {} + + auto type() const -> ParseResultType { return m_type; } + + auto remainingTokens() const -> TokenStream { return m_remainingTokens; } + + private: + ParseResultType m_type; + TokenStream m_remainingTokens; + }; + + using Result = BasicResult; + using ParserResult = BasicResult; + using InternalParseResult = BasicResult; + + struct HelpColumns { + std::string left; + std::string right; + }; + + template + inline auto convertInto(std::string const &source, T& target) -> ParserResult { + std::stringstream ss; + ss << source; + ss >> target; + if (ss.fail()) + return ParserResult::runtimeError("Unable to convert '" + source + "' to destination type"); + else + return ParserResult::ok(ParseResultType::Matched); + } + inline auto convertInto(std::string const &source, std::string& target) -> ParserResult { + target = source; + return ParserResult::ok(ParseResultType::Matched); + } + inline auto convertInto(std::string const &source, bool &target) -> ParserResult { + std::string srcLC = source; + std::transform(srcLC.begin(), srcLC.end(), srcLC.begin(), [](char c) { return static_cast( ::tolower(c) ); } ); + if (srcLC == "y" || srcLC == "1" || srcLC == "true" || srcLC == "yes" || srcLC == "on") + target = true; + else if (srcLC == "n" || srcLC == "0" || srcLC == "false" || srcLC == "no" || srcLC == "off") + target = false; + else + return ParserResult::runtimeError("Expected a boolean value but did not recognise: '" + source + "'"); + return ParserResult::ok(ParseResultType::Matched); + } + + struct BoundRefBase { + BoundRefBase() = default; + + BoundRefBase(BoundRefBase const &) = delete; + + BoundRefBase(BoundRefBase &&) = delete; + + BoundRefBase &operator=(BoundRefBase const &) = delete; + + BoundRefBase &operator=(BoundRefBase &&) = delete; + + virtual ~BoundRefBase() = default; + + virtual auto isFlag() const -> bool = 0; + + virtual auto isContainer() const -> bool { return false; } + + virtual auto setValue(std::string const &arg) -> ParserResult = 0; + + virtual auto setFlag(bool flag) -> ParserResult = 0; + }; + + struct BoundValueRefBase : BoundRefBase { + auto isFlag() const -> bool override { return false; } + + auto setFlag(bool) -> ParserResult override { + return ParserResult::logicError("Flags can only be set on boolean fields"); + } + }; + + struct BoundFlagRefBase : BoundRefBase { + auto isFlag() const -> bool override { return true; } + + auto setValue(std::string const &arg) -> ParserResult override { + bool flag; + auto result = convertInto(arg, flag); + if (result) + setFlag(flag); + return result; + } + }; + + template + struct BoundRef : BoundValueRefBase { + T &m_ref; + + explicit BoundRef(T &ref) : m_ref(ref) {} + + auto setValue(std::string const &arg) -> ParserResult override { + return convertInto(arg, m_ref); + } + }; + + template + struct BoundRef> : BoundValueRefBase { + std::vector &m_ref; + + explicit BoundRef(std::vector &ref) : m_ref(ref) {} + + auto isContainer() const -> bool override { return true; } + + auto setValue(std::string const &arg) -> ParserResult override { + T temp; + auto result = convertInto(arg, temp); + if (result) + m_ref.push_back(temp); + return result; + } + }; + + struct BoundFlagRef : BoundFlagRefBase { + bool &m_ref; + + explicit BoundFlagRef(bool &ref) : m_ref(ref) {} + + auto setFlag(bool flag) -> ParserResult override { + m_ref = flag; + return ParserResult::ok(ParseResultType::Matched); + } + }; + + template + struct LambdaInvoker { + static_assert(std::is_same::value, "Lambda must return void or clara::ParserResult"); + + template + static auto invoke(L const &lambda, ArgType const &arg) -> ParserResult { + return lambda(arg); + } + }; + + template<> + struct LambdaInvoker { + template + static auto invoke(L const &lambda, ArgType const &arg) -> ParserResult { + lambda(arg); + return ParserResult::ok(ParseResultType::Matched); + } + }; + + template + inline auto invokeLambda(L const &lambda, std::string const &arg) -> ParserResult { + ArgType temp; + auto result = convertInto(arg, temp); + return !result + ? result + : LambdaInvoker::ReturnType>::invoke(lambda, temp); + }; + + template + struct BoundLambda : BoundValueRefBase { + L m_lambda; + + static_assert( UnaryLambdaTraits::isValid, "Supplied lambda must take exactly one argument" ); + explicit BoundLambda(L const &lambda) : m_lambda(lambda) {} + + auto setValue(std::string const &arg) -> ParserResult override { + return invokeLambda::ArgType>(m_lambda, arg); + } + }; + + template + struct BoundFlagLambda : BoundFlagRefBase { + L m_lambda; + + static_assert( UnaryLambdaTraits::isValid, "Supplied lambda must take exactly one argument" ); + static_assert( std::is_same::ArgType, bool>::value, "flags must be boolean" ); + + explicit BoundFlagLambda(L const &lambda) : m_lambda(lambda) {} + + auto setFlag(bool flag) -> ParserResult override { + return LambdaInvoker::ReturnType>::invoke(m_lambda, flag); + } + }; + + enum class Optionality { + Optional, Required + }; + + struct Parser; + + class ParserBase { + public: + virtual ~ParserBase() = default; + virtual auto validate() const -> Result { return Result::ok(); } + virtual auto parse( std::string const& exeName, TokenStream const &tokens) const -> InternalParseResult = 0; + virtual auto cardinality() const -> size_t { return 1; } + + auto parse(Args const &args) const -> InternalParseResult { + return parse( args.exeName(), TokenStream(args)); + } + }; + + template + class ComposableParserImpl : public ParserBase { + public: + template + auto operator+(T const &other) const -> Parser; + }; + + // Common code and state for Args and Opts + template + class ParserRefImpl : public ComposableParserImpl { + protected: + Optionality m_optionality = Optionality::Optional; + std::shared_ptr m_ref; + std::string m_hint; + std::string m_description; + + explicit ParserRefImpl(std::shared_ptr const &ref) : m_ref(ref) {} + + public: + template + ParserRefImpl(T &ref, std::string const &hint) : m_ref(std::make_shared>(ref)), m_hint(hint) {} + + template + ParserRefImpl(LambdaT const &ref, std::string const &hint) : m_ref(std::make_shared>(ref)), + m_hint(hint) {} + + auto operator()(std::string const &description) -> DerivedT & { + m_description = description; + return static_cast( *this ); + } + + auto optional() -> DerivedT & { + m_optionality = Optionality::Optional; + return static_cast( *this ); + }; + + auto required() -> DerivedT & { + m_optionality = Optionality::Required; + return static_cast( *this ); + }; + + auto isOptional() const -> bool { + return m_optionality == Optionality::Optional; + } + + auto cardinality() const -> size_t override { + if (m_ref->isContainer()) + return 0; + else + return 1; + } + + auto hint() const -> std::string { return m_hint; } + }; + + class ExeName : public ComposableParserImpl { + std::shared_ptr m_name; + std::shared_ptr m_ref; + + template + static auto makeRef(LambdaT const &lambda) -> std::shared_ptr { + return std::make_shared>(lambda); + } + + public: + ExeName() : m_name(std::make_shared("")) {} + + explicit ExeName(std::string &ref) : ExeName() { + m_ref = std::make_shared>( ref ); + } + + template + explicit ExeName( LambdaT const& lambda ) : ExeName() { + m_ref = std::make_shared>( lambda ); + } + + // The exe name is not parsed out of the normal tokens, but is handled specially + auto parse( std::string const&, TokenStream const &tokens ) const -> InternalParseResult override { + return InternalParseResult::ok(ParseState(ParseResultType::NoMatch, tokens)); + } + + auto name() const -> std::string { return *m_name; } + auto set( std::string const& newName ) -> ParserResult { + + auto lastSlash = newName.find_last_of( "\\/" ); + auto filename = (lastSlash == std::string::npos) + ? newName + : newName.substr( lastSlash+1 ); + + *m_name = filename; + if( m_ref ) + return m_ref->setValue( filename ); + else + return ParserResult::ok( ParseResultType::Matched ); + } + }; + + class Arg : public ParserRefImpl { + public: + using ParserRefImpl::ParserRefImpl; + + auto parse(std::string const &, TokenStream const &tokens) const -> InternalParseResult override { + auto validationResult = validate(); + if (!validationResult) + return InternalParseResult(validationResult); + + auto remainingTokens = tokens; + auto const &token = *remainingTokens; + if (token.type != TokenType::Argument) + return InternalParseResult::ok(ParseState(ParseResultType::NoMatch, remainingTokens)); + + auto result = m_ref->setValue(remainingTokens->token); + if (!result) + return InternalParseResult(result); + else + return InternalParseResult::ok(ParseState(ParseResultType::Matched, ++remainingTokens)); + } + }; + + inline auto normaliseOpt(std::string const &optName) -> std::string { + if (optName[0] == '/') + return "-" + optName.substr(1); + else + return optName; + } + + class Opt : public ParserRefImpl { + protected: + std::vector m_optNames; + + public: + template + explicit Opt( LambdaT const &ref ) : ParserRefImpl(std::make_shared>(ref)) {} + + explicit Opt( bool &ref ) : ParserRefImpl(std::make_shared(ref)) {} + + template + Opt( LambdaT const &ref, std::string const &hint ) : ParserRefImpl( ref, hint ) {} + + template + Opt( T &ref, std::string const &hint ) : ParserRefImpl( ref, hint ) {} + + auto operator[](std::string const &optName) -> Opt & { + m_optNames.push_back(optName); + return *this; + } + + auto getHelpColumns() const -> std::vector { + std::ostringstream oss; + bool first = true; + for (auto const &opt : m_optNames) { + if (first) + first = false; + else + oss << ", "; + oss << opt; + } + if (!m_hint.empty()) + oss << " <" << m_hint << ">"; + return {{oss.str(), m_description}}; + } + + auto isMatch(std::string const &optToken) const -> bool { +#ifdef CLARA_PLATFORM_WINDOWS + auto normalisedToken = normaliseOpt( optToken ); +#else + auto const &normalisedToken = optToken; +#endif + for (auto const &name : m_optNames) { + if (normaliseOpt(name) == normalisedToken) + return true; + } + return false; + } + + using ParserBase::parse; + + auto parse( std::string const&, TokenStream const &tokens ) const -> InternalParseResult override { + auto validationResult = validate(); + if (!validationResult) + return InternalParseResult(validationResult); + + auto remainingTokens = tokens; + if (remainingTokens && remainingTokens->type == TokenType::Option) { + auto const &token = *remainingTokens; + if (isMatch(token.token)) { + if (m_ref->isFlag()) { + auto result = m_ref->setFlag(true); + if (!result) + return InternalParseResult(result); + if (result.value() == ParseResultType::ShortCircuitAll) + return InternalParseResult::ok(ParseState(result.value(), remainingTokens)); + } else { + ++remainingTokens; + if (!remainingTokens) + return InternalParseResult::runtimeError("Expected argument following " + token.token); + auto const &argToken = *remainingTokens; + if (argToken.type != TokenType::Argument) + return InternalParseResult::runtimeError("Expected argument following " + token.token); + auto result = m_ref->setValue(argToken.token); + if (!result) + return InternalParseResult(result); + if (result.value() == ParseResultType::ShortCircuitAll) + return InternalParseResult::ok(ParseState(result.value(), remainingTokens)); + } + return InternalParseResult::ok(ParseState(ParseResultType::Matched, ++remainingTokens)); + } + } + return InternalParseResult::ok(ParseState(ParseResultType::NoMatch, remainingTokens)); + } + + auto validate() const -> Result override { + if (m_optNames.empty()) + return Result::logicError("No options supplied to Opt"); + for (auto const &name : m_optNames) { + if (name.empty()) + return Result::logicError("Option name cannot be empty"); + if (name[0] != '-' && name[0] != '/') + return Result::logicError("Option name must begin with '-' or '/'"); + } + return ParserRefImpl::validate(); + } + }; + + struct Help : Opt { + Help( bool &showHelpFlag ) + : Opt([&]( bool flag ) { + showHelpFlag = flag; + return ParserResult::ok(ParseResultType::ShortCircuitAll); + }) + { + static_cast(*this) + ("display usage information") + ["-?"]["-h"]["--help"] + .optional(); + } + }; + + struct Parser : ParserBase { + + mutable ExeName m_exeName; + std::vector m_options; + std::vector m_args; + + auto operator+=(ExeName const &exeName) -> Parser & { + m_exeName = exeName; + return *this; + } + + auto operator+=(Arg const &arg) -> Parser & { + m_args.push_back(arg); + return *this; + } + + auto operator+=(Opt const &opt) -> Parser & { + m_options.push_back(opt); + return *this; + } + + auto operator+=(Parser const &other) -> Parser & { + m_options.insert(m_options.end(), other.m_options.begin(), other.m_options.end()); + m_args.insert(m_args.end(), other.m_args.begin(), other.m_args.end()); + return *this; + } + + template + auto operator+(T const &other) const -> Parser { + return Parser(*this) += other; + } + + auto getHelpColumns() const -> std::vector { + std::vector cols; + for (auto const &o : m_options) { + auto childCols = o.getHelpColumns(); + cols.insert(cols.end(), childCols.begin(), childCols.end()); + } + return cols; + } + + void writeToStream(std::ostream &os) const { + if (!m_exeName.name().empty()) { + os << "usage:\n" << " " << m_exeName.name() << " "; + bool required = true, first = true; + for (auto const &arg : m_args) { + if (first) + first = false; + else + os << " "; + if (arg.isOptional() && required) { + os << "["; + required = false; + } + os << "<" << arg.hint() << ">"; + if (arg.cardinality() == 0) + os << " ... "; + } + if (!required) + os << "]"; + if (!m_options.empty()) + os << " options"; + os << "\n\nwhere options are:" << std::endl; + } + + auto rows = getHelpColumns(); + size_t consoleWidth = CATCH_CLARA_CONFIG_CONSOLE_WIDTH; + size_t optWidth = 0; + for (auto const &cols : rows) + optWidth = std::max(optWidth, cols.left.size() + 2); + + for (auto const &cols : rows) { + auto row = + TextFlow::Column(cols.left).width(optWidth).indent(2) + + TextFlow::Spacer(4) + + TextFlow::Column(cols.right).width(consoleWidth - 7 - optWidth); + os << row << std::endl; + } + } + + friend auto operator<<(std::ostream &os, Parser const &parser) -> std::ostream & { + parser.writeToStream(os); + return os; + } + + auto validate() const -> Result override { + for (auto const &opt : m_options) { + auto result = opt.validate(); + if (!result) + return result; + } + for (auto const &arg : m_args) { + auto result = arg.validate(); + if (!result) + return result; + } + return Result::ok(); + } + + using ParserBase::parse; + + auto parse( std::string const& exeName, TokenStream const &tokens) const -> InternalParseResult override { + std::vector allParsers; + allParsers.reserve(m_args.size() + m_options.size()); + std::set requiredParsers; + + for (auto const &opt : m_options) { + allParsers.push_back(&opt); + if (!opt.isOptional()) + requiredParsers.insert(&opt); + } + + size_t optionalArgs = 0; + for (auto const &arg : m_args) { + allParsers.push_back(&arg); + if (!arg.isOptional()) { + if (optionalArgs > 0) + return InternalParseResult::logicError( + "Required arguments must preceed any optional arguments"); + else + ++optionalArgs; + requiredParsers.insert(&arg); + } + } + + m_exeName.set( exeName ); + + auto result = InternalParseResult::ok(ParseState(ParseResultType::NoMatch, tokens)); + while (result.value().remainingTokens()) { + auto remainingTokenCount = result.value().remainingTokens().count(); + for (auto parser : allParsers) { + result = parser->parse( exeName, result.value().remainingTokens() ); + if (!result || result.value().type() != ParseResultType::NoMatch) { + if (parser->cardinality() == 1) + allParsers.erase(std::remove(allParsers.begin(), allParsers.end(), parser), + allParsers.end()); + requiredParsers.erase(parser); + break; + } + } + if (!result || remainingTokenCount == result.value().remainingTokens().count()) + return result; + } + // !TBD Check missing required options + return result; + } + }; + + template + template + auto ComposableParserImpl::operator+(T const &other) const -> Parser { + return Parser() + static_cast( *this ) + other; + } +} // namespace detail + +// A Combined parser +using detail::Parser; + +// A parser for options +using detail::Opt; + +// A parser for arguments +using detail::Arg; + +// Wrapper for argc, argv from main() +using detail::Args; + +// Specifies the name of the executable +using detail::ExeName; + +// Convenience wrapper for option parser that specifies the help option +using detail::Help; + +// enum of result types from a parse +using detail::ParseResultType; + +// Result type for parser operation +using detail::ParserResult; + +}} // namespace Catch::clara + +// end clara.hpp +// Restore Clara's value for console width, if present +#ifdef CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH +#define CATCH_CLARA_TEXTFLOW_CONFIG_CONSOLE_WIDTH CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH +#undef CATCH_TEMP_CLARA_CONFIG_CONSOLE_WIDTH +#endif + +// end catch_clara.h +namespace Catch { + + clara::Parser makeCommandLineParser( ConfigData& config ); + +} // end namespace Catch + +// end catch_commandline.hpp +// start catch_console_colour.hpp + +namespace Catch { + + struct Colour { + enum Code { + None = 0, + + White, + Red, + Green, + Blue, + Cyan, + Yellow, + Grey, + + Bright = 0x10, + + BrightRed = Bright | Red, + BrightGreen = Bright | Green, + LightGrey = Bright | Grey, + BrightWhite = Bright | White, + + // By intention + FileName = LightGrey, + Warning = Yellow, + ResultError = BrightRed, + ResultSuccess = BrightGreen, + ResultExpectedFailure = Warning, + + Error = BrightRed, + Success = Green, + + OriginalExpression = Cyan, + ReconstructedExpression = Yellow, + + SecondaryText = LightGrey, + Headers = White + }; + + // Use constructed object for RAII guard + Colour( Code _colourCode ); + Colour( Colour&& other ) noexcept; + Colour& operator=( Colour&& other ) noexcept; + ~Colour(); + + // Use static method for one-shot changes + static void use( Code _colourCode ); + + private: + bool m_moved = false; + }; + + std::ostream& operator << ( std::ostream& os, Colour const& ); + +} // end namespace Catch + +// end catch_console_colour.hpp +// start catch_list.h + +#include + +namespace Catch { + + std::size_t listTests( Config const& config ); + + std::size_t listTestsNamesOnly( Config const& config ); + + struct TagInfo { + void add( std::string const& spelling ); + std::string all() const; + + std::set spellings; + std::size_t count = 0; + }; + + std::size_t listTags( Config const& config ); + + std::size_t listReporters( Config const& /*config*/ ); + + Option list( Config const& config ); + +} // end namespace Catch + +// end catch_list.h +// start catch_run_context.hpp + +// start catch_test_case_tracker.hpp + +#include +#include +#include + +CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS + +namespace Catch { +namespace TestCaseTracking { + + struct NameAndLocation { + std::string name; + SourceLineInfo location; + + NameAndLocation( std::string const& _name, SourceLineInfo const& _location ); + }; + + struct ITracker; + + using ITrackerPtr = std::shared_ptr; + + struct ITracker { + virtual ~ITracker() = default; + + // static queries + virtual NameAndLocation const& nameAndLocation() const = 0; + + // dynamic queries + virtual bool isComplete() const = 0; // Successfully completed or failed + virtual bool isSuccessfullyCompleted() const = 0; + virtual bool isOpen() const = 0; // Started but not complete + virtual bool hasChildren() const = 0; + + virtual ITracker& parent() = 0; + + // actions + virtual void close() = 0; // Successfully complete + virtual void fail() = 0; + virtual void markAsNeedingAnotherRun() = 0; + + virtual void addChild( ITrackerPtr const& child ) = 0; + virtual ITrackerPtr findChild( NameAndLocation const& nameAndLocation ) = 0; + virtual void openChild() = 0; + + // Debug/ checking + virtual bool isSectionTracker() const = 0; + virtual bool isIndexTracker() const = 0; + }; + + class TrackerContext { + + enum RunState { + NotStarted, + Executing, + CompletedCycle + }; + + ITrackerPtr m_rootTracker; + ITracker* m_currentTracker = nullptr; + RunState m_runState = NotStarted; + + public: + + static TrackerContext& instance(); + + ITracker& startRun(); + void endRun(); + + void startCycle(); + void completeCycle(); + + bool completedCycle() const; + ITracker& currentTracker(); + void setCurrentTracker( ITracker* tracker ); + }; + + class TrackerBase : public ITracker { + protected: + enum CycleState { + NotStarted, + Executing, + ExecutingChildren, + NeedsAnotherRun, + CompletedSuccessfully, + Failed + }; + + class TrackerHasName { + NameAndLocation m_nameAndLocation; + public: + TrackerHasName( NameAndLocation const& nameAndLocation ); + bool operator ()( ITrackerPtr const& tracker ) const; + }; + + using Children = std::vector; + NameAndLocation m_nameAndLocation; + TrackerContext& m_ctx; + ITracker* m_parent; + Children m_children; + CycleState m_runState = NotStarted; + + public: + TrackerBase( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ); + + NameAndLocation const& nameAndLocation() const override; + bool isComplete() const override; + bool isSuccessfullyCompleted() const override; + bool isOpen() const override; + bool hasChildren() const override; + + void addChild( ITrackerPtr const& child ) override; + + ITrackerPtr findChild( NameAndLocation const& nameAndLocation ) override; + ITracker& parent() override; + + void openChild() override; + + bool isSectionTracker() const override; + bool isIndexTracker() const override; + + void open(); + + void close() override; + void fail() override; + void markAsNeedingAnotherRun() override; + + private: + void moveToParent(); + void moveToThis(); + }; + + class SectionTracker : public TrackerBase { + std::vector m_filters; + public: + SectionTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ); + + bool isSectionTracker() const override; + + static SectionTracker& acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation ); + + void tryOpen(); + + void addInitialFilters( std::vector const& filters ); + void addNextFilters( std::vector const& filters ); + }; + + class IndexTracker : public TrackerBase { + int m_size; + int m_index = -1; + public: + IndexTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent, int size ); + + bool isIndexTracker() const override; + void close() override; + + static IndexTracker& acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation, int size ); + + int index() const; + + void moveNext(); + }; + +} // namespace TestCaseTracking + +using TestCaseTracking::ITracker; +using TestCaseTracking::TrackerContext; +using TestCaseTracking::SectionTracker; +using TestCaseTracking::IndexTracker; + +} // namespace Catch + +CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS + +// end catch_test_case_tracker.hpp +// start catch_fatal_condition.h + +#include + +namespace Catch { + + // Report the error condition + void reportFatal( std::string const& message ); + +} // namespace Catch + +#if defined ( CATCH_PLATFORM_WINDOWS ) ///////////////////////////////////////// +// start catch_windows_h_proxy.h + + +#if defined(CATCH_PLATFORM_WINDOWS) +# if !defined(NOMINMAX) && !defined(CATCH_CONFIG_NO_NOMINMAX) +# define CATCH_DEFINED_NOMINMAX +# define NOMINMAX +# endif +# if !defined(WIN32_LEAN_AND_MEAN) && !defined(CATCH_CONFIG_NO_WIN32_LEAN_AND_MEAN) +# define CATCH_DEFINED_WIN32_LEAN_AND_MEAN +# define WIN32_LEAN_AND_MEAN +# endif +#endif + +#ifdef __AFXDLL +#include +#else +#include +#endif + +#ifdef CATCH_DEFINED_NOMINMAX +# undef NOMINMAX +#endif +#ifdef CATCH_DEFINED_WIN32_LEAN_AND_MEAN +# undef WIN32_LEAN_AND_MEAN +#endif + +// end catch_windows_h_proxy.h + +# if !defined ( CATCH_CONFIG_WINDOWS_SEH ) + +namespace Catch { + struct FatalConditionHandler { + void reset(); + }; +} + +# else // CATCH_CONFIG_WINDOWS_SEH is defined + +namespace Catch { + + struct FatalConditionHandler { + + static LONG CALLBACK handleVectoredException(PEXCEPTION_POINTERS ExceptionInfo); + FatalConditionHandler(); + static void reset(); + ~FatalConditionHandler(); + + private: + static bool isSet; + static ULONG guaranteeSize; + static PVOID exceptionHandlerHandle; + }; + +} // namespace Catch + +# endif // CATCH_CONFIG_WINDOWS_SEH + +#else // Not Windows - assumed to be POSIX compatible ////////////////////////// + +# if !defined(CATCH_CONFIG_POSIX_SIGNALS) + +namespace Catch { + struct FatalConditionHandler { + void reset(); + }; +} + +# else // CATCH_CONFIG_POSIX_SIGNALS is defined + +#include + +namespace Catch { + + struct FatalConditionHandler { + + static bool isSet; + static struct sigaction oldSigActions[];// [sizeof(signalDefs) / sizeof(SignalDefs)]; + static stack_t oldSigStack; + static char altStackMem[]; + + static void handleSignal( int sig ); + + FatalConditionHandler(); + ~FatalConditionHandler(); + static void reset(); + }; + +} // namespace Catch + +# endif // CATCH_CONFIG_POSIX_SIGNALS + +#endif // not Windows + +// end catch_fatal_condition.h +#include + +namespace Catch { + + class StreamRedirect { + + public: + StreamRedirect(std::ostream& stream, std::string& targetString); + + ~StreamRedirect(); + + private: + std::ostream& m_stream; + std::streambuf* m_prevBuf; + std::ostringstream m_oss; + std::string& m_targetString; + }; + + // StdErr has two constituent streams in C++, std::cerr and std::clog + // This means that we need to redirect 2 streams into 1 to keep proper + // order of writes and cannot use StreamRedirect on its own + class StdErrRedirect { + public: + StdErrRedirect(std::string& targetString); + ~StdErrRedirect(); + private: + std::streambuf* m_cerrBuf; + std::streambuf* m_clogBuf; + std::ostringstream m_oss; + std::string& m_targetString; + }; + + /////////////////////////////////////////////////////////////////////////// + + class RunContext : public IResultCapture, public IRunner { + + public: + RunContext( RunContext const& ) = delete; + RunContext& operator =( RunContext const& ) = delete; + + explicit RunContext(IConfigPtr const& _config, IStreamingReporterPtr&& reporter); + + virtual ~RunContext(); + + void testGroupStarting(std::string const& testSpec, std::size_t groupIndex, std::size_t groupsCount); + void testGroupEnded(std::string const& testSpec, Totals const& totals, std::size_t groupIndex, std::size_t groupsCount); + + Totals runTest(TestCase const& testCase); + + IConfigPtr config() const; + IStreamingReporter& reporter() const; + + private: // IResultCapture + + void assertionStarting(AssertionInfo const& info) override; + void assertionEnded(AssertionResult const& result) override; + + bool sectionStarted( SectionInfo const& sectionInfo, Counts& assertions ) override; + bool testForMissingAssertions(Counts& assertions); + + void sectionEnded(SectionEndInfo const& endInfo) override; + void sectionEndedEarly(SectionEndInfo const& endInfo) override; + + void benchmarkStarting( BenchmarkInfo const& info ) override; + void benchmarkEnded( BenchmarkStats const& stats ) override; + + void pushScopedMessage(MessageInfo const& message) override; + void popScopedMessage(MessageInfo const& message) override; + + std::string getCurrentTestName() const override; + + const AssertionResult* getLastResult() const override; + + void exceptionEarlyReported() override; + + void handleFatalErrorCondition(std::string const& message) override; + + bool lastAssertionPassed() override; + + void assertionPassed() override; + + void assertionRun() override; + + public: + // !TBD We need to do this another way! + bool aborting() const override; + + private: + + void runCurrentTest(std::string& redirectedCout, std::string& redirectedCerr); + void invokeActiveTestCase(); + + private: + + void handleUnfinishedSections(); + + TestRunInfo m_runInfo; + IMutableContext& m_context; + TestCase const* m_activeTestCase = nullptr; + ITracker* m_testCaseTracker; + Option m_lastResult; + + IConfigPtr m_config; + Totals m_totals; + IStreamingReporterPtr m_reporter; + std::vector m_messages; + AssertionInfo m_lastAssertionInfo; + std::vector m_unfinishedSections; + std::vector m_activeSections; + TrackerContext m_trackerContext; + size_t m_prevPassed = 0; + bool m_shouldReportUnexpected = true; + }; + + IResultCapture& getResultCapture(); + +} // end namespace Catch + +// end catch_run_context.hpp +// start catch_version.h + +#include + +namespace Catch { + + // Versioning information + struct Version { + Version( Version const& ) = delete; + Version& operator=( Version const& ) = delete; + Version( unsigned int _majorVersion, + unsigned int _minorVersion, + unsigned int _patchNumber, + char const * const _branchName, + unsigned int _buildNumber ); + + unsigned int const majorVersion; + unsigned int const minorVersion; + unsigned int const patchNumber; + + // buildNumber is only used if branchName is not null + char const * const branchName; + unsigned int const buildNumber; + + friend std::ostream& operator << ( std::ostream& os, Version const& version ); + }; + + Version const& libraryVersion(); +} + +// end catch_version.h +// start catch_startup_exception_registry.h + +#include +#include + +namespace Catch { + + class StartupExceptionRegistry { + public: + void add(std::exception_ptr const& exception) noexcept; + std::vector const& getExceptions() const noexcept; + private: + std::vector m_exceptions; + }; + +} // end namespace Catch + +// end catch_startup_exception_registry.h +// start catch_text.h + +namespace Catch { + using namespace clara::TextFlow; +} + +// end catch_text.h +#include +#include +#include +#include + +namespace Catch { + + IStreamingReporterPtr createReporter( std::string const& reporterName, IConfigPtr const& config ) { + auto reporter = getRegistryHub().getReporterRegistry().create( reporterName, config ); + CATCH_ENFORCE( reporter, "No reporter registered with name: '" << reporterName << "'" ); + + return reporter; + } + +#ifndef CATCH_CONFIG_DEFAULT_REPORTER +#define CATCH_CONFIG_DEFAULT_REPORTER "console" +#endif + + IStreamingReporterPtr makeReporter( std::shared_ptr const& config ) { + auto const& reporterNames = config->getReporterNames(); + if( reporterNames.empty() ) + return createReporter(CATCH_CONFIG_DEFAULT_REPORTER, config ); + + IStreamingReporterPtr reporter; + for( auto const& name : reporterNames ) + addReporter( reporter, createReporter( name, config ) ); + return reporter; + } + void addListeners( IStreamingReporterPtr& reporters, IConfigPtr const& config ) { + auto const& listeners = getRegistryHub().getReporterRegistry().getListeners(); + for( auto const& listener : listeners ) + addReporter(reporters, listener->create( ReporterConfig( config ) ) ); + } + + Totals runTests( std::shared_ptr const& config ) { + + IStreamingReporterPtr reporter = makeReporter( config ); + addListeners( reporter, config ); + + RunContext context( config, std::move( reporter ) ); + + Totals totals; + + context.testGroupStarting( config->name(), 1, 1 ); + + TestSpec testSpec = config->testSpec(); + if( !testSpec.hasFilters() ) + testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "~[.]" ).testSpec(); // All not hidden tests + + std::vector const& allTestCases = getAllTestCasesSorted( *config ); + for( auto const& testCase : allTestCases ) { + if( !context.aborting() && matchTest( testCase, testSpec, *config ) ) + totals += context.runTest( testCase ); + else + context.reporter().skipTest( testCase ); + } + + context.testGroupEnded( config->name(), totals, 1, 1 ); + return totals; + } + + void applyFilenamesAsTags( IConfig const& config ) { + auto& tests = const_cast&>( getAllTestCasesSorted( config ) ); + for( auto& testCase : tests ) { + auto tags = testCase.tags; + + std::string filename = testCase.lineInfo.file; + std::string::size_type lastSlash = filename.find_last_of( "\\/" ); + if( lastSlash != std::string::npos ) + filename = filename.substr( lastSlash+1 ); + + std::string::size_type lastDot = filename.find_last_of( '.' ); + if( lastDot != std::string::npos ) + filename = filename.substr( 0, lastDot ); + + tags.push_back( '#' + filename ); + setTags( testCase, tags ); + } + } + + class Session : NonCopyable { + static const int MaxExitCode; + public: + + Session() { + static bool alreadyInstantiated = false; + if( alreadyInstantiated ) + CATCH_INTERNAL_ERROR( "Only one instance of Catch::Session can ever be used" ); + alreadyInstantiated = true; + m_cli = makeCommandLineParser( m_configData ); + } + ~Session() override { + Catch::cleanUp(); + } + + void showHelp() const { + Catch::cout() + << "\nCatch v" << libraryVersion() << "\n" + << m_cli << std::endl + << "For more detailed usage please see the project docs\n" << std::endl; + } + void libIdentify() { + Catch::cout() + << std::left << std::setw(16) << "description: " << "A Catch test executable\n" + << std::left << std::setw(16) << "category: " << "testframework\n" + << std::left << std::setw(16) << "framework: " << "Catch Test\n" + << std::left << std::setw(16) << "version: " << libraryVersion() << std::endl; + } + + int applyCommandLine( int argc, char* argv[] ) { + auto result = m_cli.parse( clara::Args( argc, argv ) ); + if( !result ) { + Catch::cerr() + << Colour( Colour::Red ) + << "\nError(s) in input:\n" + << Column( result.errorMessage() ).indent( 2 ) + << "\n\n"; + Catch::cerr() << "Run with -? for usage\n" << std::endl; + return MaxExitCode; + } + + if( m_configData.showHelp ) + showHelp(); + if( m_configData.libIdentify ) + libIdentify(); + m_config.reset(); + return 0; + } + + void useConfigData( ConfigData const& configData ) { + m_configData = configData; + m_config.reset(); + } + + int run( int argc, char* argv[] ) { + const auto& exceptions = getRegistryHub().getStartupExceptionRegistry().getExceptions(); + if ( !exceptions.empty() ) { + Catch::cerr() << "Errors occured during startup!" << '\n'; + // iterate over all exceptions and notify user + for ( const auto& ex_ptr : exceptions ) { + try { + std::rethrow_exception(ex_ptr); + } catch ( std::exception const& ex ) { + Catch::cerr() << ex.what() << '\n'; + } + } + return 1; + } + int returnCode = applyCommandLine( argc, argv ); + if( returnCode == 0 ) + returnCode = run(); + return returnCode; + } + + #if defined(WIN32) && defined(UNICODE) + int run( int argc, wchar_t* const argv[] ) { + + char **utf8Argv = new char *[ argc ]; + + for ( int i = 0; i < argc; ++i ) { + int bufSize = WideCharToMultiByte( CP_UTF8, 0, argv[i], -1, NULL, 0, NULL, NULL ); + + utf8Argv[ i ] = new char[ bufSize ]; + + WideCharToMultiByte( CP_UTF8, 0, argv[i], -1, utf8Argv[i], bufSize, NULL, NULL ); + } + + int returnCode = run( argc, utf8Argv ); + + for ( int i = 0; i < argc; ++i ) + delete [] utf8Argv[ i ]; + + delete [] utf8Argv; + + return returnCode; + } + #endif + int run() { + if( ( m_configData.waitForKeypress & WaitForKeypress::BeforeStart ) != 0 ) { + Catch::cout() << "...waiting for enter/ return before starting" << std::endl; + std::getchar(); + } + int exitCode = runInternal(); + if( ( m_configData.waitForKeypress & WaitForKeypress::BeforeExit ) != 0 ) { + Catch::cout() << "...waiting for enter/ return before exiting, with code: " << exitCode << std::endl; + std::getchar(); + } + return exitCode; + } + + clara::Parser const& cli() const { + return m_cli; + } + void cli( clara::Parser const& newParser ) { + m_cli = newParser; + } + ConfigData& configData() { + return m_configData; + } + Config& config() { + if( !m_config ) + m_config = std::make_shared( m_configData ); + return *m_config; + } + private: + int runInternal() { + if( m_configData.showHelp || m_configData.libIdentify ) + return 0; + + try + { + config(); // Force config to be constructed + + seedRng( *m_config ); + + if( m_configData.filenamesAsTags ) + applyFilenamesAsTags( *m_config ); + + // Handle list request + if( Option listed = list( config() ) ) + return static_cast( *listed ); + + return (std::min)( MaxExitCode, static_cast( runTests( m_config ).assertions.failed ) ); + } + catch( std::exception& ex ) { + Catch::cerr() << ex.what() << std::endl; + return MaxExitCode; + } + } + + clara::Parser m_cli; + ConfigData m_configData; + std::shared_ptr m_config; + }; + + const int Session::MaxExitCode = 255; + +} // end namespace Catch + +// end catch_session.hpp +// Cpp files will be included in the single-header file here +// start catch_approx.cpp + +#include + +namespace Catch { +namespace Detail { + + double max(double lhs, double rhs) { + if (lhs < rhs) { + return rhs; + } + return lhs; + } + + Approx::Approx ( double value ) + : m_epsilon( std::numeric_limits::epsilon()*100 ), + m_margin( 0.0 ), + m_scale( 1.0 ), + m_value( value ) + {} + + Approx Approx::custom() { + return Approx( 0 ); + } + + std::string Approx::toString() const { + std::ostringstream oss; + oss << "Approx( " << ::Catch::Detail::stringify( m_value ) << " )"; + return oss.str(); + } + +} // end namespace Detail + +std::string StringMaker::convert(Catch::Detail::Approx const& value) { + return value.toString(); +} + +} // end namespace Catch +// end catch_approx.cpp +// start catch_assertionhandler.cpp + +#include + +namespace Catch { + + auto operator <<( std::ostream& os, ITransientExpression const& expr ) -> std::ostream& { + expr.streamReconstructedExpression( os ); + return os; + } + + LazyExpression::LazyExpression( bool isNegated ) + : m_isNegated( isNegated ) + {} + + LazyExpression::LazyExpression( LazyExpression const& other ) : m_isNegated( other.m_isNegated ) {} + + LazyExpression::operator bool() const { + return m_transientExpression != nullptr; + } + + auto operator << ( std::ostream& os, LazyExpression const& lazyExpr ) -> std::ostream& { + if( lazyExpr.m_isNegated ) + os << "!"; + + if( lazyExpr ) { + if( lazyExpr.m_isNegated && lazyExpr.m_transientExpression->isBinaryExpression() ) + os << "(" << *lazyExpr.m_transientExpression << ")"; + else + os << *lazyExpr.m_transientExpression; + } + else { + os << "{** error - unchecked empty expression requested **}"; + } + return os; + } + + AssertionHandler::AssertionHandler + ( StringRef macroName, + SourceLineInfo const& lineInfo, + StringRef capturedExpression, + ResultDisposition::Flags resultDisposition ) + : m_assertionInfo{ macroName, lineInfo, capturedExpression, resultDisposition } + { + getCurrentContext().getResultCapture()->assertionStarting( m_assertionInfo ); + } + AssertionHandler::~AssertionHandler() { + if ( m_inExceptionGuard ) { + handle( ResultWas::ThrewException, "Exception translation was disabled by CATCH_CONFIG_FAST_COMPILE" ); + getCurrentContext().getResultCapture()->exceptionEarlyReported(); + } + } + + void AssertionHandler::handle( ITransientExpression const& expr ) { + + bool negated = isFalseTest( m_assertionInfo.resultDisposition ); + bool result = expr.getResult() != negated; + + handle( result ? ResultWas::Ok : ResultWas::ExpressionFailed, &expr, negated ); + } + void AssertionHandler::handle( ResultWas::OfType resultType ) { + handle( resultType, nullptr, false ); + } + void AssertionHandler::handle( ResultWas::OfType resultType, StringRef const& message ) { + AssertionResultData data( resultType, LazyExpression( false ) ); + data.message = message; + handle( data, nullptr ); + } + void AssertionHandler::handle( ResultWas::OfType resultType, ITransientExpression const* expr, bool negated ) { + AssertionResultData data( resultType, LazyExpression( negated ) ); + handle( data, expr ); + } + void AssertionHandler::handle( AssertionResultData const& resultData, ITransientExpression const* expr ) { + + getResultCapture().assertionRun(); + + AssertionResult assertionResult{ m_assertionInfo, resultData }; + assertionResult.m_resultData.lazyExpression.m_transientExpression = expr; + + getResultCapture().assertionEnded( assertionResult ); + + if( !assertionResult.isOk() ) { + m_shouldDebugBreak = getCurrentContext().getConfig()->shouldDebugBreak(); + m_shouldThrow = + getCurrentContext().getRunner()->aborting() || + (m_assertionInfo.resultDisposition & ResultDisposition::Normal); + } + } + + auto AssertionHandler::allowThrows() const -> bool { + return getCurrentContext().getConfig()->allowThrows(); + } + + auto AssertionHandler::shouldDebugBreak() const -> bool { + return m_shouldDebugBreak; + } + void AssertionHandler::reactWithDebugBreak() const { + if (m_shouldDebugBreak) { + /////////////////////////////////////////////////////////////////// + // To inspect the state during test, you need to go one level up the callstack + // To go back to the test and change execution, jump over the reactWithoutDebugBreak() call + /////////////////////////////////////////////////////////////////// + CATCH_BREAK_INTO_DEBUGGER(); + } + reactWithoutDebugBreak(); + } + void AssertionHandler::reactWithoutDebugBreak() const { + if( m_shouldThrow ) + throw Catch::TestFailureException(); + } + + void AssertionHandler::useActiveException() { + handle( ResultWas::ThrewException, Catch::translateActiveException() ); + } + + void AssertionHandler::setExceptionGuard() { + assert( m_inExceptionGuard == false ); + m_inExceptionGuard = true; + } + void AssertionHandler::unsetExceptionGuard() { + assert( m_inExceptionGuard == true ); + m_inExceptionGuard = false; + } + + // This is the overload that takes a string and infers the Equals matcher from it + // The more general overload, that takes any string matcher, is in catch_capture_matchers.cpp + void handleExceptionMatchExpr( AssertionHandler& handler, std::string const& str, StringRef matcherString ) { + handleExceptionMatchExpr( handler, Matchers::Equals( str ), matcherString ); + } + +} // namespace Catch +// end catch_assertionhandler.cpp +// start catch_assertionresult.cpp + +namespace Catch { + + std::string AssertionResultData::reconstructExpression() const { + + if( reconstructedExpression.empty() ) { + if( lazyExpression ) { + // !TBD Use stringstream for now, but rework above to pass stream in + std::ostringstream oss; + oss << lazyExpression; + reconstructedExpression = oss.str(); + } + } + return reconstructedExpression; + } + + AssertionResult::AssertionResult( AssertionInfo const& info, AssertionResultData const& data ) + : m_info( info ), + m_resultData( data ) + {} + + // Result was a success + bool AssertionResult::succeeded() const { + return Catch::isOk( m_resultData.resultType ); + } + + // Result was a success, or failure is suppressed + bool AssertionResult::isOk() const { + return Catch::isOk( m_resultData.resultType ) || shouldSuppressFailure( m_info.resultDisposition ); + } + + ResultWas::OfType AssertionResult::getResultType() const { + return m_resultData.resultType; + } + + bool AssertionResult::hasExpression() const { + return m_info.capturedExpression[0] != 0; + } + + bool AssertionResult::hasMessage() const { + return !m_resultData.message.empty(); + } + + std::string AssertionResult::getExpression() const { + if (isFalseTest(m_info.resultDisposition)) + return '!' + std::string(m_info.capturedExpression); + else + return m_info.capturedExpression; + } + + std::string AssertionResult::getExpressionInMacro() const { + std::string expr; + if( m_info.macroName[0] == 0 ) + expr = m_info.capturedExpression; + else { + expr.reserve( m_info.macroName.size() + m_info.capturedExpression.size() + 4 ); + expr += m_info.macroName; + expr += "( "; + expr += m_info.capturedExpression; + expr += " )"; + } + return expr; + } + + bool AssertionResult::hasExpandedExpression() const { + return hasExpression() && getExpandedExpression() != getExpression(); + } + + std::string AssertionResult::getExpandedExpression() const { + std::string expr = m_resultData.reconstructExpression(); + return expr.empty() + ? getExpression() + : expr; + } + + std::string AssertionResult::getMessage() const { + return m_resultData.message; + } + SourceLineInfo AssertionResult::getSourceInfo() const { + return m_info.lineInfo; + } + + std::string AssertionResult::getTestMacroName() const { + return m_info.macroName; + } + +} // end namespace Catch +// end catch_assertionresult.cpp +// start catch_benchmark.cpp + +namespace Catch { + + auto BenchmarkLooper::getResolution() -> uint64_t { + return getEstimatedClockResolution() * getCurrentContext().getConfig()->benchmarkResolutionMultiple(); + } + + void BenchmarkLooper::reportStart() { + getResultCapture().benchmarkStarting( { m_name } ); + } + auto BenchmarkLooper::needsMoreIterations() -> bool { + auto elapsed = m_timer.getElapsedNanoseconds(); + + // Exponentially increasing iterations until we're confident in our timer resolution + if( elapsed < m_resolution ) { + m_iterationsToRun *= 10; + return true; + } + + getResultCapture().benchmarkEnded( { { m_name }, m_count, elapsed } ); + return false; + } + +} // end namespace Catch +// end catch_benchmark.cpp +// start catch_capture_matchers.cpp + +namespace Catch { + + using StringMatcher = Matchers::Impl::MatcherBase; + + // This is the general overload that takes a any string matcher + // There is another overload, in catch_assertinhandler.h/.cpp, that only takes a string and infers + // the Equals matcher (so the header does not mention matchers) + void handleExceptionMatchExpr( AssertionHandler& handler, StringMatcher const& matcher, StringRef matcherString ) { + std::string exceptionMessage = Catch::translateActiveException(); + MatchExpr expr( exceptionMessage, matcher, matcherString ); + handler.handle( expr ); + } + +} // namespace Catch +// end catch_capture_matchers.cpp +// start catch_commandline.cpp + +#include +#include + +namespace Catch { + + clara::Parser makeCommandLineParser( ConfigData& config ) { + + using namespace clara; + + auto const setWarning = [&]( std::string const& warning ) { + if( warning != "NoAssertions" ) + return ParserResult::runtimeError( "Unrecognised warning: '" + warning + "'" ); + config.warnings = static_cast( config.warnings | WarnAbout::NoAssertions ); + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const loadTestNamesFromFile = [&]( std::string const& filename ) { + std::ifstream f( filename.c_str() ); + if( !f.is_open() ) + return ParserResult::runtimeError( "Unable to load input file: '" + filename + "'" ); + + std::string line; + while( std::getline( f, line ) ) { + line = trim(line); + if( !line.empty() && !startsWith( line, '#' ) ) { + if( !startsWith( line, '"' ) ) + line = '"' + line + '"'; + config.testsOrTags.push_back( line + ',' ); + } + } + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const setTestOrder = [&]( std::string const& order ) { + if( startsWith( "declared", order ) ) + config.runOrder = RunTests::InDeclarationOrder; + else if( startsWith( "lexical", order ) ) + config.runOrder = RunTests::InLexicographicalOrder; + else if( startsWith( "random", order ) ) + config.runOrder = RunTests::InRandomOrder; + else + return clara::ParserResult::runtimeError( "Unrecognised ordering: '" + order + "'" ); + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const setRngSeed = [&]( std::string const& seed ) { + if( seed != "time" ) + return clara::detail::convertInto( seed, config.rngSeed ); + config.rngSeed = static_cast( std::time(nullptr) ); + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const setColourUsage = [&]( std::string const& useColour ) { + auto mode = toLower( useColour ); + + if( mode == "yes" ) + config.useColour = UseColour::Yes; + else if( mode == "no" ) + config.useColour = UseColour::No; + else if( mode == "auto" ) + config.useColour = UseColour::Auto; + else + return ParserResult::runtimeError( "colour mode must be one of: auto, yes or no. '" + useColour + "' not recognised" ); + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const setWaitForKeypress = [&]( std::string const& keypress ) { + auto keypressLc = toLower( keypress ); + if( keypressLc == "start" ) + config.waitForKeypress = WaitForKeypress::BeforeStart; + else if( keypressLc == "exit" ) + config.waitForKeypress = WaitForKeypress::BeforeExit; + else if( keypressLc == "both" ) + config.waitForKeypress = WaitForKeypress::BeforeStartAndExit; + else + return ParserResult::runtimeError( "keypress argument must be one of: start, exit or both. '" + keypress + "' not recognised" ); + return ParserResult::ok( ParseResultType::Matched ); + }; + auto const setVerbosity = [&]( std::string const& verbosity ) { + auto lcVerbosity = toLower( verbosity ); + if( lcVerbosity == "quiet" ) + config.verbosity = Verbosity::Quiet; + else if( lcVerbosity == "normal" ) + config.verbosity = Verbosity::Normal; + else if( lcVerbosity == "high" ) + config.verbosity = Verbosity::High; + else + return ParserResult::runtimeError( "Unrecognised verbosity, '" + verbosity + "'" ); + return ParserResult::ok( ParseResultType::Matched ); + }; + + auto cli + = ExeName( config.processName ) + + Help( config.showHelp ) + + Opt( config.listTests ) + ["-l"]["--list-tests"] + ( "list all/matching test cases" ) + + Opt( config.listTags ) + ["-t"]["--list-tags"] + ( "list all/matching tags" ) + + Opt( config.showSuccessfulTests ) + ["-s"]["--success"] + ( "include successful tests in output" ) + + Opt( config.shouldDebugBreak ) + ["-b"]["--break"] + ( "break into debugger on failure" ) + + Opt( config.noThrow ) + ["-e"]["--nothrow"] + ( "skip exception tests" ) + + Opt( config.showInvisibles ) + ["-i"]["--invisibles"] + ( "show invisibles (tabs, newlines)" ) + + Opt( config.outputFilename, "filename" ) + ["-o"]["--out"] + ( "output filename" ) + + Opt( config.reporterNames, "name" ) + ["-r"]["--reporter"] + ( "reporter to use (defaults to console)" ) + + Opt( config.name, "name" ) + ["-n"]["--name"] + ( "suite name" ) + + Opt( [&]( bool ){ config.abortAfter = 1; } ) + ["-a"]["--abort"] + ( "abort at first failure" ) + + Opt( [&]( int x ){ config.abortAfter = x; }, "no. failures" ) + ["-x"]["--abortx"] + ( "abort after x failures" ) + + Opt( setWarning, "warning name" ) + ["-w"]["--warn"] + ( "enable warnings" ) + + Opt( [&]( bool flag ) { config.showDurations = flag ? ShowDurations::Always : ShowDurations::Never; }, "yes|no" ) + ["-d"]["--durations"] + ( "show test durations" ) + + Opt( loadTestNamesFromFile, "filename" ) + ["-f"]["--input-file"] + ( "load test names to run from a file" ) + + Opt( config.filenamesAsTags ) + ["-#"]["--filenames-as-tags"] + ( "adds a tag for the filename" ) + + Opt( config.sectionsToRun, "section name" ) + ["-c"]["--section"] + ( "specify section to run" ) + + Opt( setVerbosity, "quiet|normal|high" ) + ["-v"]["--verbosity"] + ( "set output verbosity" ) + + Opt( config.listTestNamesOnly ) + ["--list-test-names-only"] + ( "list all/matching test cases names only" ) + + Opt( config.listReporters ) + ["--list-reporters"] + ( "list all reporters" ) + + Opt( setTestOrder, "decl|lex|rand" ) + ["--order"] + ( "test case order (defaults to decl)" ) + + Opt( setRngSeed, "'time'|number" ) + ["--rng-seed"] + ( "set a specific seed for random numbers" ) + + Opt( setColourUsage, "yes|no" ) + ["--use-colour"] + ( "should output be colourised" ) + + Opt( config.libIdentify ) + ["--libidentify"] + ( "report name and version according to libidentify standard" ) + + Opt( setWaitForKeypress, "start|exit|both" ) + ["--wait-for-keypress"] + ( "waits for a keypress before exiting" ) + + Opt( config.benchmarkResolutionMultiple, "multiplier" ) + ["--benchmark-resolution-multiple"] + ( "multiple of clock resolution to run benchmarks" ) + + + Arg( config.testsOrTags, "test name|pattern|tags" ) + ( "which test or tests to use" ); + + return cli; + } + +} // end namespace Catch +// end catch_commandline.cpp +// start catch_common.cpp + +#include +#include + +namespace Catch { + + SourceLineInfo::SourceLineInfo( char const* _file, std::size_t _line ) noexcept + : file( _file ), + line( _line ) + {} + bool SourceLineInfo::empty() const noexcept { + return file[0] == '\0'; + } + bool SourceLineInfo::operator == ( SourceLineInfo const& other ) const noexcept { + return line == other.line && (file == other.file || std::strcmp(file, other.file) == 0); + } + bool SourceLineInfo::operator < ( SourceLineInfo const& other ) const noexcept { + return line < other.line || ( line == other.line && (std::strcmp(file, other.file) < 0)); + } + + void seedRng( IConfig const& config ) { + if( config.rngSeed() != 0 ) + std::srand( config.rngSeed() ); + } + unsigned int rngSeed() { + return getCurrentContext().getConfig()->rngSeed(); + } + + std::ostream& operator << ( std::ostream& os, SourceLineInfo const& info ) { +#ifndef __GNUG__ + os << info.file << '(' << info.line << ')'; +#else + os << info.file << ':' << info.line; +#endif + return os; + } + + bool isTrue( bool value ){ return value; } + bool alwaysTrue() { return true; } + bool alwaysFalse() { return false; } + + std::string StreamEndStop::operator+() const { + return std::string(); + } + +} +// end catch_common.cpp +// start catch_config.cpp + +namespace Catch { + + Config::Config( ConfigData const& data ) + : m_data( data ), + m_stream( openStream() ) + { + if( !data.testsOrTags.empty() ) { + TestSpecParser parser( ITagAliasRegistry::get() ); + for( auto const& testOrTags : data.testsOrTags ) + parser.parse( testOrTags ); + m_testSpec = parser.testSpec(); + } + } + + std::string const& Config::getFilename() const { + return m_data.outputFilename ; + } + + bool Config::listTests() const { return m_data.listTests; } + bool Config::listTestNamesOnly() const { return m_data.listTestNamesOnly; } + bool Config::listTags() const { return m_data.listTags; } + bool Config::listReporters() const { return m_data.listReporters; } + + std::string Config::getProcessName() const { return m_data.processName; } + + std::vector const& Config::getReporterNames() const { return m_data.reporterNames; } + std::vector const& Config::getSectionsToRun() const { return m_data.sectionsToRun; } + + TestSpec const& Config::testSpec() const { return m_testSpec; } + + bool Config::showHelp() const { return m_data.showHelp; } + + // IConfig interface + bool Config::allowThrows() const { return !m_data.noThrow; } + std::ostream& Config::stream() const { return m_stream->stream(); } + std::string Config::name() const { return m_data.name.empty() ? m_data.processName : m_data.name; } + bool Config::includeSuccessfulResults() const { return m_data.showSuccessfulTests; } + bool Config::warnAboutMissingAssertions() const { return m_data.warnings & WarnAbout::NoAssertions; } + ShowDurations::OrNot Config::showDurations() const { return m_data.showDurations; } + RunTests::InWhatOrder Config::runOrder() const { return m_data.runOrder; } + unsigned int Config::rngSeed() const { return m_data.rngSeed; } + int Config::benchmarkResolutionMultiple() const { return m_data.benchmarkResolutionMultiple; } + UseColour::YesOrNo Config::useColour() const { return m_data.useColour; } + bool Config::shouldDebugBreak() const { return m_data.shouldDebugBreak; } + int Config::abortAfter() const { return m_data.abortAfter; } + bool Config::showInvisibles() const { return m_data.showInvisibles; } + Verbosity Config::verbosity() const { return m_data.verbosity; } + + IStream const* Config::openStream() { + if( m_data.outputFilename.empty() ) + return new CoutStream(); + else if( m_data.outputFilename[0] == '%' ) { + if( m_data.outputFilename == "%debug" ) + return new DebugOutStream(); + else + CATCH_ERROR( "Unrecognised stream: '" << m_data.outputFilename << "'" ); + } + else + return new FileStream( m_data.outputFilename ); + } + +} // end namespace Catch +// end catch_config.cpp +// start catch_console_colour.cpp + +// start catch_errno_guard.h + +namespace Catch { + + class ErrnoGuard { + public: + ErrnoGuard(); + ~ErrnoGuard(); + private: + int m_oldErrno; + }; + +} + +// end catch_errno_guard.h +namespace Catch { + namespace { + + struct IColourImpl { + virtual ~IColourImpl() = default; + virtual void use( Colour::Code _colourCode ) = 0; + }; + + struct NoColourImpl : IColourImpl { + void use( Colour::Code ) {} + + static IColourImpl* instance() { + static NoColourImpl s_instance; + return &s_instance; + } + }; + + } // anon namespace +} // namespace Catch + +#if !defined( CATCH_CONFIG_COLOUR_NONE ) && !defined( CATCH_CONFIG_COLOUR_WINDOWS ) && !defined( CATCH_CONFIG_COLOUR_ANSI ) +# ifdef CATCH_PLATFORM_WINDOWS +# define CATCH_CONFIG_COLOUR_WINDOWS +# else +# define CATCH_CONFIG_COLOUR_ANSI +# endif +#endif + +#if defined ( CATCH_CONFIG_COLOUR_WINDOWS ) ///////////////////////////////////////// + +namespace Catch { +namespace { + + class Win32ColourImpl : public IColourImpl { + public: + Win32ColourImpl() : stdoutHandle( GetStdHandle(STD_OUTPUT_HANDLE) ) + { + CONSOLE_SCREEN_BUFFER_INFO csbiInfo; + GetConsoleScreenBufferInfo( stdoutHandle, &csbiInfo ); + originalForegroundAttributes = csbiInfo.wAttributes & ~( BACKGROUND_GREEN | BACKGROUND_RED | BACKGROUND_BLUE | BACKGROUND_INTENSITY ); + originalBackgroundAttributes = csbiInfo.wAttributes & ~( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE | FOREGROUND_INTENSITY ); + } + + virtual void use( Colour::Code _colourCode ) override { + switch( _colourCode ) { + case Colour::None: return setTextAttribute( originalForegroundAttributes ); + case Colour::White: return setTextAttribute( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE ); + case Colour::Red: return setTextAttribute( FOREGROUND_RED ); + case Colour::Green: return setTextAttribute( FOREGROUND_GREEN ); + case Colour::Blue: return setTextAttribute( FOREGROUND_BLUE ); + case Colour::Cyan: return setTextAttribute( FOREGROUND_BLUE | FOREGROUND_GREEN ); + case Colour::Yellow: return setTextAttribute( FOREGROUND_RED | FOREGROUND_GREEN ); + case Colour::Grey: return setTextAttribute( 0 ); + + case Colour::LightGrey: return setTextAttribute( FOREGROUND_INTENSITY ); + case Colour::BrightRed: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_RED ); + case Colour::BrightGreen: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_GREEN ); + case Colour::BrightWhite: return setTextAttribute( FOREGROUND_INTENSITY | FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE ); + + case Colour::Bright: CATCH_INTERNAL_ERROR( "not a colour" ); + } + } + + private: + void setTextAttribute( WORD _textAttribute ) { + SetConsoleTextAttribute( stdoutHandle, _textAttribute | originalBackgroundAttributes ); + } + HANDLE stdoutHandle; + WORD originalForegroundAttributes; + WORD originalBackgroundAttributes; + }; + + IColourImpl* platformColourInstance() { + static Win32ColourImpl s_instance; + + IConfigPtr config = getCurrentContext().getConfig(); + UseColour::YesOrNo colourMode = config + ? config->useColour() + : UseColour::Auto; + if( colourMode == UseColour::Auto ) + colourMode = UseColour::Yes; + return colourMode == UseColour::Yes + ? &s_instance + : NoColourImpl::instance(); + } + +} // end anon namespace +} // end namespace Catch + +#elif defined( CATCH_CONFIG_COLOUR_ANSI ) ////////////////////////////////////// + +#include + +namespace Catch { +namespace { + + // use POSIX/ ANSI console terminal codes + // Thanks to Adam Strzelecki for original contribution + // (http://github.com/nanoant) + // https://github.com/philsquared/Catch/pull/131 + class PosixColourImpl : public IColourImpl { + public: + virtual void use( Colour::Code _colourCode ) override { + switch( _colourCode ) { + case Colour::None: + case Colour::White: return setColour( "[0m" ); + case Colour::Red: return setColour( "[0;31m" ); + case Colour::Green: return setColour( "[0;32m" ); + case Colour::Blue: return setColour( "[0;34m" ); + case Colour::Cyan: return setColour( "[0;36m" ); + case Colour::Yellow: return setColour( "[0;33m" ); + case Colour::Grey: return setColour( "[1;30m" ); + + case Colour::LightGrey: return setColour( "[0;37m" ); + case Colour::BrightRed: return setColour( "[1;31m" ); + case Colour::BrightGreen: return setColour( "[1;32m" ); + case Colour::BrightWhite: return setColour( "[1;37m" ); + + case Colour::Bright: CATCH_INTERNAL_ERROR( "not a colour" ); + } + } + static IColourImpl* instance() { + static PosixColourImpl s_instance; + return &s_instance; + } + + private: + void setColour( const char* _escapeCode ) { + Catch::cout() << '\033' << _escapeCode; + } + }; + + IColourImpl* platformColourInstance() { + ErrnoGuard guard; + IConfigPtr config = getCurrentContext().getConfig(); + UseColour::YesOrNo colourMode = config + ? config->useColour() + : UseColour::Auto; + if( colourMode == UseColour::Auto ) + colourMode = isatty(STDOUT_FILENO) + ? UseColour::Yes + : UseColour::No; + return colourMode == UseColour::Yes + ? PosixColourImpl::instance() + : NoColourImpl::instance(); + } + +} // end anon namespace +} // end namespace Catch + +#else // not Windows or ANSI /////////////////////////////////////////////// + +namespace Catch { + + static IColourImpl* platformColourInstance() { return NoColourImpl::instance(); } + +} // end namespace Catch + +#endif // Windows/ ANSI/ None + +namespace Catch { + + Colour::Colour( Code _colourCode ) { use( _colourCode ); } + Colour::Colour( Colour&& rhs ) noexcept { + m_moved = rhs.m_moved; + rhs.m_moved = true; + } + Colour& Colour::operator=( Colour&& rhs ) noexcept { + m_moved = rhs.m_moved; + rhs.m_moved = true; + return *this; + } + + Colour::~Colour(){ if( !m_moved ) use( None ); } + + void Colour::use( Code _colourCode ) { + static IColourImpl* impl = platformColourInstance(); + impl->use( _colourCode ); + } + + std::ostream& operator << ( std::ostream& os, Colour const& ) { + return os; + } + +} // end namespace Catch +// end catch_console_colour.cpp +// start catch_context.cpp + +namespace Catch { + + class Context : public IMutableContext, NonCopyable { + + public: // IContext + virtual IResultCapture* getResultCapture() override { + return m_resultCapture; + } + virtual IRunner* getRunner() override { + return m_runner; + } + + virtual IConfigPtr getConfig() const override { + return m_config; + } + + public: // IMutableContext + virtual void setResultCapture( IResultCapture* resultCapture ) override { + m_resultCapture = resultCapture; + } + virtual void setRunner( IRunner* runner ) override { + m_runner = runner; + } + virtual void setConfig( IConfigPtr const& config ) override { + m_config = config; + } + + friend IMutableContext& getCurrentMutableContext(); + + private: + IConfigPtr m_config; + IRunner* m_runner = nullptr; + IResultCapture* m_resultCapture = nullptr; + }; + + namespace { + Context* currentContext = nullptr; + } + IMutableContext& getCurrentMutableContext() { + if( !currentContext ) + currentContext = new Context(); + return *currentContext; + } + IContext& getCurrentContext() { + return getCurrentMutableContext(); + } + + void cleanUpContext() { + delete currentContext; + currentContext = nullptr; + } +} +// end catch_context.cpp +// start catch_debugger.cpp + +#ifdef CATCH_PLATFORM_MAC + + #include + #include + #include + #include + #include + + namespace Catch{ + + // The following function is taken directly from the following technical note: + // http://developer.apple.com/library/mac/#qa/qa2004/qa1361.html + + // Returns true if the current process is being debugged (either + // running under the debugger or has a debugger attached post facto). + bool isDebuggerActive(){ + + int mib[4]; + struct kinfo_proc info; + size_t size; + + // Initialize the flags so that, if sysctl fails for some bizarre + // reason, we get a predictable result. + + info.kp_proc.p_flag = 0; + + // Initialize mib, which tells sysctl the info we want, in this case + // we're looking for information about a specific process ID. + + mib[0] = CTL_KERN; + mib[1] = KERN_PROC; + mib[2] = KERN_PROC_PID; + mib[3] = getpid(); + + // Call sysctl. + + size = sizeof(info); + if( sysctl(mib, sizeof(mib) / sizeof(*mib), &info, &size, nullptr, 0) != 0 ) { + Catch::cerr() << "\n** Call to sysctl failed - unable to determine if debugger is active **\n" << std::endl; + return false; + } + + // We're being debugged if the P_TRACED flag is set. + + return ( (info.kp_proc.p_flag & P_TRACED) != 0 ); + } + } // namespace Catch + +#elif defined(CATCH_PLATFORM_LINUX) + #include + #include + + namespace Catch{ + // The standard POSIX way of detecting a debugger is to attempt to + // ptrace() the process, but this needs to be done from a child and not + // this process itself to still allow attaching to this process later + // if wanted, so is rather heavy. Under Linux we have the PID of the + // "debugger" (which doesn't need to be gdb, of course, it could also + // be strace, for example) in /proc/$PID/status, so just get it from + // there instead. + bool isDebuggerActive(){ + // Libstdc++ has a bug, where std::ifstream sets errno to 0 + // This way our users can properly assert over errno values + ErrnoGuard guard; + std::ifstream in("/proc/self/status"); + for( std::string line; std::getline(in, line); ) { + static const int PREFIX_LEN = 11; + if( line.compare(0, PREFIX_LEN, "TracerPid:\t") == 0 ) { + // We're traced if the PID is not 0 and no other PID starts + // with 0 digit, so it's enough to check for just a single + // character. + return line.length() > PREFIX_LEN && line[PREFIX_LEN] != '0'; + } + } + + return false; + } + } // namespace Catch +#elif defined(_MSC_VER) + extern "C" __declspec(dllimport) int __stdcall IsDebuggerPresent(); + namespace Catch { + bool isDebuggerActive() { + return IsDebuggerPresent() != 0; + } + } +#elif defined(__MINGW32__) + extern "C" __declspec(dllimport) int __stdcall IsDebuggerPresent(); + namespace Catch { + bool isDebuggerActive() { + return IsDebuggerPresent() != 0; + } + } +#else + namespace Catch { + bool isDebuggerActive() { return false; } + } +#endif // Platform + +#ifdef CATCH_PLATFORM_WINDOWS + + namespace Catch { + void writeToDebugConsole( std::string const& text ) { + ::OutputDebugStringA( text.c_str() ); + } + } +#else + namespace Catch { + void writeToDebugConsole( std::string const& text ) { + // !TBD: Need a version for Mac/ XCode and other IDEs + Catch::cout() << text; + } + } +#endif // Platform +// end catch_debugger.cpp +// start catch_decomposer.cpp + +namespace Catch { + + void formatReconstructedExpression( std::ostream &os, std::string const& lhs, std::string const& op, std::string const& rhs ) { + if( lhs.size() + rhs.size() < 40 && + lhs.find('\n') == std::string::npos && + rhs.find('\n') == std::string::npos ) + os << lhs << " " << op << " " << rhs; + else + os << lhs << "\n" << op << "\n" << rhs; + } +} +// end catch_decomposer.cpp +// start catch_errno_guard.cpp + +#include + +namespace Catch { + ErrnoGuard::ErrnoGuard():m_oldErrno(errno){} + ErrnoGuard::~ErrnoGuard() { errno = m_oldErrno; } +} +// end catch_errno_guard.cpp +// start catch_exception_translator_registry.cpp + +// start catch_exception_translator_registry.h + +#include +#include +#include + +namespace Catch { + + class ExceptionTranslatorRegistry : public IExceptionTranslatorRegistry { + public: + ~ExceptionTranslatorRegistry(); + virtual void registerTranslator( const IExceptionTranslator* translator ); + virtual std::string translateActiveException() const override; + std::string tryTranslators() const; + + private: + std::vector> m_translators; + }; +} + +// end catch_exception_translator_registry.h +#ifdef __OBJC__ +#import "Foundation/Foundation.h" +#endif + +namespace Catch { + + ExceptionTranslatorRegistry::~ExceptionTranslatorRegistry() { + } + + void ExceptionTranslatorRegistry::registerTranslator( const IExceptionTranslator* translator ) { + m_translators.push_back( std::unique_ptr( translator ) ); + } + + std::string ExceptionTranslatorRegistry::translateActiveException() const { + try { +#ifdef __OBJC__ + // In Objective-C try objective-c exceptions first + @try { + return tryTranslators(); + } + @catch (NSException *exception) { + return Catch::toString( [exception description] ); + } +#else + return tryTranslators(); +#endif + } + catch( TestFailureException& ) { + throw; + } + catch( std::exception& ex ) { + return ex.what(); + } + catch( std::string& msg ) { + return msg; + } + catch( const char* msg ) { + return msg; + } + catch(...) { + return "Unknown exception"; + } + } + + std::string ExceptionTranslatorRegistry::tryTranslators() const { + if( m_translators.empty() ) + throw; + else + return m_translators[0]->translate( m_translators.begin()+1, m_translators.end() ); + } +} +// end catch_exception_translator_registry.cpp +// start catch_fatal_condition.cpp + +namespace Catch { + + // Report the error condition + void reportFatal( std::string const& message ) { + IContext& context = Catch::getCurrentContext(); + IResultCapture* resultCapture = context.getResultCapture(); + resultCapture->handleFatalErrorCondition( message ); + } + +} // namespace Catch + +#if defined ( CATCH_PLATFORM_WINDOWS ) ///////////////////////////////////////// + +# if !defined ( CATCH_CONFIG_WINDOWS_SEH ) + +namespace Catch { + void FatalConditionHandler::reset() {} +} + +# else // CATCH_CONFIG_WINDOWS_SEH is defined + +namespace Catch { + struct SignalDefs { DWORD id; const char* name; }; + + // There is no 1-1 mapping between signals and windows exceptions. + // Windows can easily distinguish between SO and SigSegV, + // but SigInt, SigTerm, etc are handled differently. + SignalDefs signalDefs[] = { + { EXCEPTION_ILLEGAL_INSTRUCTION, "SIGILL - Illegal instruction signal" }, + { EXCEPTION_STACK_OVERFLOW, "SIGSEGV - Stack overflow" }, + { EXCEPTION_ACCESS_VIOLATION, "SIGSEGV - Segmentation violation signal" }, + { EXCEPTION_INT_DIVIDE_BY_ZERO, "Divide by zero error" }, + }; + + LONG CALLBACK FatalConditionHandler::handleVectoredException(PEXCEPTION_POINTERS ExceptionInfo) { + for (int i = 0; i < sizeof(signalDefs) / sizeof(SignalDefs); ++i) { + if (ExceptionInfo->ExceptionRecord->ExceptionCode == signalDefs[i].id) { + reportFatal(signalDefs[i].name); + } + } + // If its not an exception we care about, pass it along. + // This stops us from eating debugger breaks etc. + return EXCEPTION_CONTINUE_SEARCH; + } + + FatalConditionHandler::FatalConditionHandler() { + isSet = true; + // 32k seems enough for Catch to handle stack overflow, + // but the value was found experimentally, so there is no strong guarantee + guaranteeSize = 32 * 1024; + exceptionHandlerHandle = nullptr; + // Register as first handler in current chain + exceptionHandlerHandle = AddVectoredExceptionHandler(1, handleVectoredException); + // Pass in guarantee size to be filled + SetThreadStackGuarantee(&guaranteeSize); + } + + void FatalConditionHandler::reset() { + if (isSet) { + // Unregister handler and restore the old guarantee + RemoveVectoredExceptionHandler(exceptionHandlerHandle); + SetThreadStackGuarantee(&guaranteeSize); + exceptionHandlerHandle = nullptr; + isSet = false; + } + } + + FatalConditionHandler::~FatalConditionHandler() { + reset(); + } + +bool FatalConditionHandler::isSet = false; +ULONG FatalConditionHandler::guaranteeSize = 0; +PVOID FatalConditionHandler::exceptionHandlerHandle = nullptr; + +} // namespace Catch + +# endif // CATCH_CONFIG_WINDOWS_SEH + +#else // Not Windows - assumed to be POSIX compatible ////////////////////////// + +# if !defined(CATCH_CONFIG_POSIX_SIGNALS) + +namespace Catch { + void FatalConditionHandler::reset() {} +} + +# else // CATCH_CONFIG_POSIX_SIGNALS is defined + +#include + +namespace Catch { + + struct SignalDefs { + int id; + const char* name; + }; + SignalDefs signalDefs[] = { + { SIGINT, "SIGINT - Terminal interrupt signal" }, + { SIGILL, "SIGILL - Illegal instruction signal" }, + { SIGFPE, "SIGFPE - Floating point error signal" }, + { SIGSEGV, "SIGSEGV - Segmentation violation signal" }, + { SIGTERM, "SIGTERM - Termination request signal" }, + { SIGABRT, "SIGABRT - Abort (abnormal termination) signal" } + }; + + void FatalConditionHandler::handleSignal( int sig ) { + std::string name = ""; + for (std::size_t i = 0; i < sizeof(signalDefs) / sizeof(SignalDefs); ++i) { + SignalDefs &def = signalDefs[i]; + if (sig == def.id) { + name = def.name; + break; + } + } + reset(); + reportFatal(name); + raise( sig ); + } + + FatalConditionHandler::FatalConditionHandler() { + isSet = true; + stack_t sigStack; + sigStack.ss_sp = altStackMem; + sigStack.ss_size = SIGSTKSZ; + sigStack.ss_flags = 0; + sigaltstack(&sigStack, &oldSigStack); + struct sigaction sa = { }; + + sa.sa_handler = handleSignal; + sa.sa_flags = SA_ONSTACK; + for (std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i) { + sigaction(signalDefs[i].id, &sa, &oldSigActions[i]); + } + } + + FatalConditionHandler::~FatalConditionHandler() { + reset(); + } + + void FatalConditionHandler::reset() { + if( isSet ) { + // Set signals back to previous values -- hopefully nobody overwrote them in the meantime + for( std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i ) { + sigaction(signalDefs[i].id, &oldSigActions[i], nullptr); + } + // Return the old stack + sigaltstack(&oldSigStack, nullptr); + isSet = false; + } + } + + bool FatalConditionHandler::isSet = false; + struct sigaction FatalConditionHandler::oldSigActions[sizeof(signalDefs)/sizeof(SignalDefs)] = {}; + stack_t FatalConditionHandler::oldSigStack = {}; + char FatalConditionHandler::altStackMem[SIGSTKSZ] = {}; + +} // namespace Catch + +# endif // CATCH_CONFIG_POSIX_SIGNALS + +#endif // not Windows +// end catch_fatal_condition.cpp +// start catch_interfaces_reporter.cpp + +// start catch_reporter_multi.h + +namespace Catch { + + class MultipleReporters : public IStreamingReporter { + using Reporters = std::vector; + Reporters m_reporters; + + public: + void add( IStreamingReporterPtr&& reporter ); + + public: // IStreamingReporter + + ReporterPreferences getPreferences() const override; + + void noMatchingTestCases( std::string const& spec ) override; + + static std::set getSupportedVerbosities(); + + void testRunStarting( TestRunInfo const& testRunInfo ) override; + void testGroupStarting( GroupInfo const& groupInfo ) override; + void testCaseStarting( TestCaseInfo const& testInfo ) override; + void sectionStarting( SectionInfo const& sectionInfo ) override; + void assertionStarting( AssertionInfo const& assertionInfo ) override; + + // The return value indicates if the messages buffer should be cleared: + bool assertionEnded( AssertionStats const& assertionStats ) override; + void sectionEnded( SectionStats const& sectionStats ) override; + void testCaseEnded( TestCaseStats const& testCaseStats ) override; + void testGroupEnded( TestGroupStats const& testGroupStats ) override; + void testRunEnded( TestRunStats const& testRunStats ) override; + + void skipTest( TestCaseInfo const& testInfo ) override; + bool isMulti() const override; + + }; + +} // end namespace Catch +// end catch_reporter_multi.h +namespace Catch { + + ReporterConfig::ReporterConfig( IConfigPtr const& _fullConfig ) + : m_stream( &_fullConfig->stream() ), m_fullConfig( _fullConfig ) {} + + ReporterConfig::ReporterConfig( IConfigPtr const& _fullConfig, std::ostream& _stream ) + : m_stream( &_stream ), m_fullConfig( _fullConfig ) {} + + std::ostream& ReporterConfig::stream() const { return *m_stream; } + IConfigPtr ReporterConfig::fullConfig() const { return m_fullConfig; } + + TestRunInfo::TestRunInfo( std::string const& _name ) : name( _name ) {} + + GroupInfo::GroupInfo( std::string const& _name, + std::size_t _groupIndex, + std::size_t _groupsCount ) + : name( _name ), + groupIndex( _groupIndex ), + groupsCounts( _groupsCount ) + {} + + AssertionStats::AssertionStats( AssertionResult const& _assertionResult, + std::vector const& _infoMessages, + Totals const& _totals ) + : assertionResult( _assertionResult ), + infoMessages( _infoMessages ), + totals( _totals ) + { + assertionResult.m_resultData.lazyExpression.m_transientExpression = _assertionResult.m_resultData.lazyExpression.m_transientExpression; + + if( assertionResult.hasMessage() ) { + // Copy message into messages list. + // !TBD This should have been done earlier, somewhere + MessageBuilder builder( assertionResult.getTestMacroName(), assertionResult.getSourceInfo(), assertionResult.getResultType() ); + builder << assertionResult.getMessage(); + builder.m_info.message = builder.m_stream.str(); + + infoMessages.push_back( builder.m_info ); + } + } + + SectionStats::SectionStats( SectionInfo const& _sectionInfo, + Counts const& _assertions, + double _durationInSeconds, + bool _missingAssertions ) + : sectionInfo( _sectionInfo ), + assertions( _assertions ), + durationInSeconds( _durationInSeconds ), + missingAssertions( _missingAssertions ) + {} + + TestCaseStats::TestCaseStats( TestCaseInfo const& _testInfo, + Totals const& _totals, + std::string const& _stdOut, + std::string const& _stdErr, + bool _aborting ) + : testInfo( _testInfo ), + totals( _totals ), + stdOut( _stdOut ), + stdErr( _stdErr ), + aborting( _aborting ) + {} + + TestGroupStats::TestGroupStats( GroupInfo const& _groupInfo, + Totals const& _totals, + bool _aborting ) + : groupInfo( _groupInfo ), + totals( _totals ), + aborting( _aborting ) + {} + + TestGroupStats::TestGroupStats( GroupInfo const& _groupInfo ) + : groupInfo( _groupInfo ), + aborting( false ) + {} + + TestRunStats::TestRunStats( TestRunInfo const& _runInfo, + Totals const& _totals, + bool _aborting ) + : runInfo( _runInfo ), + totals( _totals ), + aborting( _aborting ) + {} + + bool IStreamingReporter::isMulti() const { return false; } + + void addReporter( IStreamingReporterPtr& existingReporter, IStreamingReporterPtr&& additionalReporter ) { + + if( !existingReporter ) { + existingReporter = std::move( additionalReporter ); + return; + } + + MultipleReporters* multi = nullptr; + + if( existingReporter->isMulti() ) { + multi = static_cast( existingReporter.get() ); + } + else { + auto newMulti = std::unique_ptr( new MultipleReporters ); + newMulti->add( std::move( existingReporter ) ); + multi = newMulti.get(); + existingReporter = std::move( newMulti ); + } + multi->add( std::move( additionalReporter ) ); + } + +} // end namespace Catch +// end catch_interfaces_reporter.cpp +// start catch_leak_detector.cpp + +namespace Catch { + +#ifdef CATCH_CONFIG_WINDOWS_CRTDBG +#include + + LeakDetector::LeakDetector() { + int flag = _CrtSetDbgFlag(_CRTDBG_REPORT_FLAG); + flag |= _CRTDBG_LEAK_CHECK_DF; + flag |= _CRTDBG_ALLOC_MEM_DF; + _CrtSetDbgFlag(flag); + _CrtSetReportMode(_CRT_WARN, _CRTDBG_MODE_FILE | _CRTDBG_MODE_DEBUG); + _CrtSetReportFile(_CRT_WARN, _CRTDBG_FILE_STDERR); + // Change this to leaking allocation's number to break there + _CrtSetBreakAlloc(-1); + } + +#else + + LeakDetector::LeakDetector(){} + +#endif + +} +// end catch_leak_detector.cpp +// start catch_list.cpp + +#include +#include +#include + +namespace Catch { + + std::size_t listTests( Config const& config ) { + TestSpec testSpec = config.testSpec(); + if( config.testSpec().hasFilters() ) + Catch::cout() << "Matching test cases:\n"; + else { + Catch::cout() << "All available test cases:\n"; + testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec(); + } + + auto matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); + for( auto const& testCaseInfo : matchedTestCases ) { + Colour::Code colour = testCaseInfo.isHidden() + ? Colour::SecondaryText + : Colour::None; + Colour colourGuard( colour ); + + Catch::cout() << Column( testCaseInfo.name ).initialIndent( 2 ).indent( 4 ) << "\n"; + if( config.verbosity() >= Verbosity::High ) { + Catch::cout() << Column( Catch::Detail::stringify( testCaseInfo.lineInfo ) ).indent(4) << std::endl; + std::string description = testCaseInfo.description; + if( description.empty() ) + description = "(NO DESCRIPTION)"; + Catch::cout() << Column( description ).indent(4) << std::endl; + } + if( !testCaseInfo.tags.empty() ) + Catch::cout() << Column( testCaseInfo.tagsAsString() ).indent( 6 ) << "\n"; + } + + if( !config.testSpec().hasFilters() ) + Catch::cout() << pluralise( matchedTestCases.size(), "test case" ) << '\n' << std::endl; + else + Catch::cout() << pluralise( matchedTestCases.size(), "matching test case" ) << '\n' << std::endl; + return matchedTestCases.size(); + } + + std::size_t listTestsNamesOnly( Config const& config ) { + TestSpec testSpec = config.testSpec(); + if( !config.testSpec().hasFilters() ) + testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec(); + std::size_t matchedTests = 0; + std::vector matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); + for( auto const& testCaseInfo : matchedTestCases ) { + matchedTests++; + if( startsWith( testCaseInfo.name, '#' ) ) + Catch::cout() << '"' << testCaseInfo.name << '"'; + else + Catch::cout() << testCaseInfo.name; + if ( config.verbosity() >= Verbosity::High ) + Catch::cout() << "\t@" << testCaseInfo.lineInfo; + Catch::cout() << std::endl; + } + return matchedTests; + } + + void TagInfo::add( std::string const& spelling ) { + ++count; + spellings.insert( spelling ); + } + + std::string TagInfo::all() const { + std::string out; + for( auto const& spelling : spellings ) + out += "[" + spelling + "]"; + return out; + } + + std::size_t listTags( Config const& config ) { + TestSpec testSpec = config.testSpec(); + if( config.testSpec().hasFilters() ) + Catch::cout() << "Tags for matching test cases:\n"; + else { + Catch::cout() << "All available tags:\n"; + testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec(); + } + + std::map tagCounts; + + std::vector matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config ); + for( auto const& testCase : matchedTestCases ) { + for( auto const& tagName : testCase.getTestCaseInfo().tags ) { + std::string lcaseTagName = toLower( tagName ); + auto countIt = tagCounts.find( lcaseTagName ); + if( countIt == tagCounts.end() ) + countIt = tagCounts.insert( std::make_pair( lcaseTagName, TagInfo() ) ).first; + countIt->second.add( tagName ); + } + } + + for( auto const& tagCount : tagCounts ) { + std::ostringstream oss; + oss << " " << std::setw(2) << tagCount.second.count << " "; + auto wrapper = Column( tagCount.second.all() ) + .initialIndent( 0 ) + .indent( oss.str().size() ) + .width( CATCH_CONFIG_CONSOLE_WIDTH-10 ); + Catch::cout() << oss.str() << wrapper << '\n'; + } + Catch::cout() << pluralise( tagCounts.size(), "tag" ) << '\n' << std::endl; + return tagCounts.size(); + } + + std::size_t listReporters( Config const& /*config*/ ) { + Catch::cout() << "Available reporters:\n"; + IReporterRegistry::FactoryMap const& factories = getRegistryHub().getReporterRegistry().getFactories(); + std::size_t maxNameLen = 0; + for( auto const& factoryKvp : factories ) + maxNameLen = (std::max)( maxNameLen, factoryKvp.first.size() ); + + for( auto const& factoryKvp : factories ) { + Catch::cout() + << Column( factoryKvp.first + ":" ) + .indent(2) + .width( 5+maxNameLen ) + + Column( factoryKvp.second->getDescription() ) + .initialIndent(0) + .indent(2) + .width( CATCH_CONFIG_CONSOLE_WIDTH - maxNameLen-8 ) + << "\n"; + } + Catch::cout() << std::endl; + return factories.size(); + } + + Option list( Config const& config ) { + Option listedCount; + if( config.listTests() ) + listedCount = listedCount.valueOr(0) + listTests( config ); + if( config.listTestNamesOnly() ) + listedCount = listedCount.valueOr(0) + listTestsNamesOnly( config ); + if( config.listTags() ) + listedCount = listedCount.valueOr(0) + listTags( config ); + if( config.listReporters() ) + listedCount = listedCount.valueOr(0) + listReporters( config ); + return listedCount; + } + +} // end namespace Catch +// end catch_list.cpp +// start catch_matchers.cpp + +namespace Catch { +namespace Matchers { + namespace Impl { + + std::string MatcherUntypedBase::toString() const { + if( m_cachedToString.empty() ) + m_cachedToString = describe(); + return m_cachedToString; + } + + } // namespace Impl +} // namespace Matchers + +using namespace Matchers; +using Matchers::Impl::MatcherBase; + +} // namespace Catch +// end catch_matchers.cpp +// start catch_matchers_string.cpp + +namespace Catch { +namespace Matchers { + + namespace StdString { + + CasedString::CasedString( std::string const& str, CaseSensitive::Choice caseSensitivity ) + : m_caseSensitivity( caseSensitivity ), + m_str( adjustString( str ) ) + {} + std::string CasedString::adjustString( std::string const& str ) const { + return m_caseSensitivity == CaseSensitive::No + ? toLower( str ) + : str; + } + std::string CasedString::caseSensitivitySuffix() const { + return m_caseSensitivity == CaseSensitive::No + ? " (case insensitive)" + : std::string(); + } + + StringMatcherBase::StringMatcherBase( std::string const& operation, CasedString const& comparator ) + : m_comparator( comparator ), + m_operation( operation ) { + } + + std::string StringMatcherBase::describe() const { + std::string description; + description.reserve(5 + m_operation.size() + m_comparator.m_str.size() + + m_comparator.caseSensitivitySuffix().size()); + description += m_operation; + description += ": \""; + description += m_comparator.m_str; + description += "\""; + description += m_comparator.caseSensitivitySuffix(); + return description; + } + + EqualsMatcher::EqualsMatcher( CasedString const& comparator ) : StringMatcherBase( "equals", comparator ) {} + + bool EqualsMatcher::match( std::string const& source ) const { + return m_comparator.adjustString( source ) == m_comparator.m_str; + } + + ContainsMatcher::ContainsMatcher( CasedString const& comparator ) : StringMatcherBase( "contains", comparator ) {} + + bool ContainsMatcher::match( std::string const& source ) const { + return contains( m_comparator.adjustString( source ), m_comparator.m_str ); + } + + StartsWithMatcher::StartsWithMatcher( CasedString const& comparator ) : StringMatcherBase( "starts with", comparator ) {} + + bool StartsWithMatcher::match( std::string const& source ) const { + return startsWith( m_comparator.adjustString( source ), m_comparator.m_str ); + } + + EndsWithMatcher::EndsWithMatcher( CasedString const& comparator ) : StringMatcherBase( "ends with", comparator ) {} + + bool EndsWithMatcher::match( std::string const& source ) const { + return endsWith( m_comparator.adjustString( source ), m_comparator.m_str ); + } + + } // namespace StdString + + StdString::EqualsMatcher Equals( std::string const& str, CaseSensitive::Choice caseSensitivity ) { + return StdString::EqualsMatcher( StdString::CasedString( str, caseSensitivity) ); + } + StdString::ContainsMatcher Contains( std::string const& str, CaseSensitive::Choice caseSensitivity ) { + return StdString::ContainsMatcher( StdString::CasedString( str, caseSensitivity) ); + } + StdString::EndsWithMatcher EndsWith( std::string const& str, CaseSensitive::Choice caseSensitivity ) { + return StdString::EndsWithMatcher( StdString::CasedString( str, caseSensitivity) ); + } + StdString::StartsWithMatcher StartsWith( std::string const& str, CaseSensitive::Choice caseSensitivity ) { + return StdString::StartsWithMatcher( StdString::CasedString( str, caseSensitivity) ); + } + +} // namespace Matchers +} // namespace Catch +// end catch_matchers_string.cpp +// start catch_message.cpp + +namespace Catch { + + MessageInfo::MessageInfo( std::string const& _macroName, + SourceLineInfo const& _lineInfo, + ResultWas::OfType _type ) + : macroName( _macroName ), + lineInfo( _lineInfo ), + type( _type ), + sequence( ++globalCount ) + {} + + bool MessageInfo::operator==( MessageInfo const& other ) const { + return sequence == other.sequence; + } + + bool MessageInfo::operator<( MessageInfo const& other ) const { + return sequence < other.sequence; + } + + // This may need protecting if threading support is added + unsigned int MessageInfo::globalCount = 0; + + //////////////////////////////////////////////////////////////////////////// + + Catch::MessageBuilder::MessageBuilder( std::string const& macroName, + SourceLineInfo const& lineInfo, + ResultWas::OfType type ) + :m_info(macroName, lineInfo, type) {} + + //////////////////////////////////////////////////////////////////////////// + + ScopedMessage::ScopedMessage( MessageBuilder const& builder ) + : m_info( builder.m_info ) + { + m_info.message = builder.m_stream.str(); + getResultCapture().pushScopedMessage( m_info ); + } + + ScopedMessage::~ScopedMessage() { + if ( !std::uncaught_exception() ){ + getResultCapture().popScopedMessage(m_info); + } + } + +} // end namespace Catch +// end catch_message.cpp +// start catch_notimplemented_exception.cpp + +#include + +namespace Catch { + + NotImplementedException::NotImplementedException( SourceLineInfo const& lineInfo ) { + std::ostringstream oss; + oss << lineInfo << ": function "; + oss << "not implemented"; + m_what = oss.str(); + } + + const char* NotImplementedException::what() const noexcept { + return m_what.c_str(); + } + +} // end namespace Catch +// end catch_notimplemented_exception.cpp +// start catch_registry_hub.cpp + +// start catch_test_case_registry_impl.hpp + +#include +#include +#include +#include + +namespace Catch { + + class TestCase; + struct IConfig; + + struct RandomNumberGenerator { + using result_type = std::ptrdiff_t; + + result_type operator()( result_type n ) const; + + static constexpr result_type min() { return 0; } + static constexpr result_type max() { return 1000000; } + result_type operator()() const; + template + static void shuffle( V& vector ) { + RandomNumberGenerator rng; + std::shuffle( vector.begin(), vector.end(), rng ); + } + }; + + std::vector sortTests( IConfig const& config, std::vector const& unsortedTestCases ); + bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ); + + void enforceNoDuplicateTestCases( std::vector const& functions ); + + std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ); + std::vector const& getAllTestCasesSorted( IConfig const& config ); + + class TestRegistry : public ITestCaseRegistry { + public: + virtual ~TestRegistry() = default; + + virtual void registerTest( TestCase const& testCase ); + + std::vector const& getAllTests() const override; + std::vector const& getAllTestsSorted( IConfig const& config ) const override; + + private: + std::vector m_functions; + mutable RunTests::InWhatOrder m_currentSortOrder = RunTests::InDeclarationOrder; + mutable std::vector m_sortedFunctions; + size_t m_unnamedCount = 0; + std::ios_base::Init m_ostreamInit; // Forces cout/ cerr to be initialised + }; + + /////////////////////////////////////////////////////////////////////////// + + class TestInvokerAsFunction : public ITestInvoker { + void(*m_testAsFunction)(); + public: + TestInvokerAsFunction( void(*testAsFunction)() ) noexcept; + + void invoke() const override; + }; + + std::string extractClassName( std::string const& classOrQualifiedMethodName ); + + /////////////////////////////////////////////////////////////////////////// + +} // end namespace Catch + +// end catch_test_case_registry_impl.hpp +// start catch_reporter_registry.hpp + +#include + +namespace Catch { + + class ReporterRegistry : public IReporterRegistry { + + public: + + ~ReporterRegistry() override {} + + IStreamingReporterPtr create( std::string const& name, IConfigPtr const& config ) const override { + FactoryMap::const_iterator it = m_factories.find( name ); + if( it == m_factories.end() ) + return nullptr; + return it->second->create( ReporterConfig( config ) ); + } + + void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) { + m_factories.insert( { name, factory } ); + } + void registerListener( IReporterFactoryPtr const& factory ) { + m_listeners.push_back( factory ); + } + + FactoryMap const& getFactories() const override { + return m_factories; + } + Listeners const& getListeners() const override { + return m_listeners; + } + + private: + FactoryMap m_factories; + Listeners m_listeners; + }; +} + +// end catch_reporter_registry.hpp +// start catch_tag_alias_registry.h + +// start catch_tag_alias.h + +#include + +namespace Catch { + + struct TagAlias { + TagAlias(std::string const& _tag, SourceLineInfo _lineInfo); + + std::string tag; + SourceLineInfo lineInfo; + }; + +} // end namespace Catch + +// end catch_tag_alias.h +#include + +namespace Catch { + + class TagAliasRegistry : public ITagAliasRegistry { + public: + ~TagAliasRegistry() override; + TagAlias const* find( std::string const& alias ) const override; + std::string expandAliases( std::string const& unexpandedTestSpec ) const override; + void add( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ); + + private: + std::map m_registry; + }; + +} // end namespace Catch + +// end catch_tag_alias_registry.h +namespace Catch { + + namespace { + + class RegistryHub : public IRegistryHub, public IMutableRegistryHub, + private NonCopyable { + + public: // IRegistryHub + RegistryHub() { + } + IReporterRegistry const& getReporterRegistry() const override { + return m_reporterRegistry; + } + ITestCaseRegistry const& getTestCaseRegistry() const override { + return m_testCaseRegistry; + } + IExceptionTranslatorRegistry& getExceptionTranslatorRegistry() override { + return m_exceptionTranslatorRegistry; + } + ITagAliasRegistry const& getTagAliasRegistry() const override { + return m_tagAliasRegistry; + } + StartupExceptionRegistry const& getStartupExceptionRegistry() const override { + return m_exceptionRegistry; + } + + public: // IMutableRegistryHub + void registerReporter( std::string const& name, IReporterFactoryPtr const& factory ) override { + m_reporterRegistry.registerReporter( name, factory ); + } + void registerListener( IReporterFactoryPtr const& factory ) override { + m_reporterRegistry.registerListener( factory ); + } + void registerTest( TestCase const& testInfo ) override { + m_testCaseRegistry.registerTest( testInfo ); + } + void registerTranslator( const IExceptionTranslator* translator ) override { + m_exceptionTranslatorRegistry.registerTranslator( translator ); + } + void registerTagAlias( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) override { + m_tagAliasRegistry.add( alias, tag, lineInfo ); + } + void registerStartupException() noexcept override { + m_exceptionRegistry.add(std::current_exception()); + } + + private: + TestRegistry m_testCaseRegistry; + ReporterRegistry m_reporterRegistry; + ExceptionTranslatorRegistry m_exceptionTranslatorRegistry; + TagAliasRegistry m_tagAliasRegistry; + StartupExceptionRegistry m_exceptionRegistry; + }; + + // Single, global, instance + RegistryHub*& getTheRegistryHub() { + static RegistryHub* theRegistryHub = nullptr; + if( !theRegistryHub ) + theRegistryHub = new RegistryHub(); + return theRegistryHub; + } + } + + IRegistryHub& getRegistryHub() { + return *getTheRegistryHub(); + } + IMutableRegistryHub& getMutableRegistryHub() { + return *getTheRegistryHub(); + } + void cleanUp() { + delete getTheRegistryHub(); + getTheRegistryHub() = nullptr; + cleanUpContext(); + } + std::string translateActiveException() { + return getRegistryHub().getExceptionTranslatorRegistry().translateActiveException(); + } + +} // end namespace Catch +// end catch_registry_hub.cpp +// start catch_result_type.cpp + +namespace Catch { + + bool isOk( ResultWas::OfType resultType ) { + return ( resultType & ResultWas::FailureBit ) == 0; + } + bool isJustInfo( int flags ) { + return flags == ResultWas::Info; + } + + ResultDisposition::Flags operator | ( ResultDisposition::Flags lhs, ResultDisposition::Flags rhs ) { + return static_cast( static_cast( lhs ) | static_cast( rhs ) ); + } + + bool shouldContinueOnFailure( int flags ) { return ( flags & ResultDisposition::ContinueOnFailure ) != 0; } + bool isFalseTest( int flags ) { return ( flags & ResultDisposition::FalseTest ) != 0; } + bool shouldSuppressFailure( int flags ) { return ( flags & ResultDisposition::SuppressFail ) != 0; } + +} // end namespace Catch +// end catch_result_type.cpp +// start catch_run_context.cpp + +#include +#include + +namespace Catch { + + StreamRedirect::StreamRedirect(std::ostream& stream, std::string& targetString) + : m_stream(stream), + m_prevBuf(stream.rdbuf()), + m_targetString(targetString) { + stream.rdbuf(m_oss.rdbuf()); + } + + StreamRedirect::~StreamRedirect() { + m_targetString += m_oss.str(); + m_stream.rdbuf(m_prevBuf); + } + + StdErrRedirect::StdErrRedirect(std::string & targetString) + :m_cerrBuf(cerr().rdbuf()), m_clogBuf(clog().rdbuf()), + m_targetString(targetString) { + cerr().rdbuf(m_oss.rdbuf()); + clog().rdbuf(m_oss.rdbuf()); + } + + StdErrRedirect::~StdErrRedirect() { + m_targetString += m_oss.str(); + cerr().rdbuf(m_cerrBuf); + clog().rdbuf(m_clogBuf); + } + + RunContext::RunContext(IConfigPtr const& _config, IStreamingReporterPtr&& reporter) + : m_runInfo(_config->name()), + m_context(getCurrentMutableContext()), + m_config(_config), + m_reporter(std::move(reporter)), + m_lastAssertionInfo{ "", SourceLineInfo("",0), "", ResultDisposition::Normal } + { + m_context.setRunner(this); + m_context.setConfig(m_config); + m_context.setResultCapture(this); + m_reporter->testRunStarting(m_runInfo); + } + + RunContext::~RunContext() { + m_reporter->testRunEnded(TestRunStats(m_runInfo, m_totals, aborting())); + } + + void RunContext::testGroupStarting(std::string const& testSpec, std::size_t groupIndex, std::size_t groupsCount) { + m_reporter->testGroupStarting(GroupInfo(testSpec, groupIndex, groupsCount)); + } + + void RunContext::testGroupEnded(std::string const& testSpec, Totals const& totals, std::size_t groupIndex, std::size_t groupsCount) { + m_reporter->testGroupEnded(TestGroupStats(GroupInfo(testSpec, groupIndex, groupsCount), totals, aborting())); + } + + Totals RunContext::runTest(TestCase const& testCase) { + Totals prevTotals = m_totals; + + std::string redirectedCout; + std::string redirectedCerr; + + TestCaseInfo testInfo = testCase.getTestCaseInfo(); + + m_reporter->testCaseStarting(testInfo); + + m_activeTestCase = &testCase; + + ITracker& rootTracker = m_trackerContext.startRun(); + assert(rootTracker.isSectionTracker()); + static_cast(rootTracker).addInitialFilters(m_config->getSectionsToRun()); + do { + m_trackerContext.startCycle(); + m_testCaseTracker = &SectionTracker::acquire(m_trackerContext, TestCaseTracking::NameAndLocation(testInfo.name, testInfo.lineInfo)); + runCurrentTest(redirectedCout, redirectedCerr); + } while (!m_testCaseTracker->isSuccessfullyCompleted() && !aborting()); + + Totals deltaTotals = m_totals.delta(prevTotals); + if (testInfo.expectedToFail() && deltaTotals.testCases.passed > 0) { + deltaTotals.assertions.failed++; + deltaTotals.testCases.passed--; + deltaTotals.testCases.failed++; + } + m_totals.testCases += deltaTotals.testCases; + m_reporter->testCaseEnded(TestCaseStats(testInfo, + deltaTotals, + redirectedCout, + redirectedCerr, + aborting())); + + m_activeTestCase = nullptr; + m_testCaseTracker = nullptr; + + return deltaTotals; + } + + IConfigPtr RunContext::config() const { + return m_config; + } + + IStreamingReporter& RunContext::reporter() const { + return *m_reporter; + } + + void RunContext::assertionStarting(AssertionInfo const& info) { + m_reporter->assertionStarting( info ); + } + void RunContext::assertionEnded(AssertionResult const & result) { + if (result.getResultType() == ResultWas::Ok) { + m_totals.assertions.passed++; + } else if (!result.isOk()) { + m_totals.assertions.failed++; + } + + // We have no use for the return value (whether messages should be cleared), because messages were made scoped + // and should be let to clear themselves out. + static_cast(m_reporter->assertionEnded(AssertionStats(result, m_messages, m_totals))); + + // Reset working state + m_lastAssertionInfo = { "", m_lastAssertionInfo.lineInfo, "{Unknown expression after the reported line}", m_lastAssertionInfo.resultDisposition }; + m_lastResult = result; + } + + bool RunContext::sectionStarted(SectionInfo const & sectionInfo, Counts & assertions) { + ITracker& sectionTracker = SectionTracker::acquire(m_trackerContext, TestCaseTracking::NameAndLocation(sectionInfo.name, sectionInfo.lineInfo)); + if (!sectionTracker.isOpen()) + return false; + m_activeSections.push_back(§ionTracker); + + m_lastAssertionInfo.lineInfo = sectionInfo.lineInfo; + + m_reporter->sectionStarting(sectionInfo); + + assertions = m_totals.assertions; + + return true; + } + + bool RunContext::testForMissingAssertions(Counts& assertions) { + if (assertions.total() != 0) + return false; + if (!m_config->warnAboutMissingAssertions()) + return false; + if (m_trackerContext.currentTracker().hasChildren()) + return false; + m_totals.assertions.failed++; + assertions.failed++; + return true; + } + + void RunContext::sectionEnded(SectionEndInfo const & endInfo) { + Counts assertions = m_totals.assertions - endInfo.prevAssertions; + bool missingAssertions = testForMissingAssertions(assertions); + + if (!m_activeSections.empty()) { + m_activeSections.back()->close(); + m_activeSections.pop_back(); + } + + m_reporter->sectionEnded(SectionStats(endInfo.sectionInfo, assertions, endInfo.durationInSeconds, missingAssertions)); + m_messages.clear(); + } + + void RunContext::sectionEndedEarly(SectionEndInfo const & endInfo) { + if (m_unfinishedSections.empty()) + m_activeSections.back()->fail(); + else + m_activeSections.back()->close(); + m_activeSections.pop_back(); + + m_unfinishedSections.push_back(endInfo); + } + void RunContext::benchmarkStarting( BenchmarkInfo const& info ) { + m_reporter->benchmarkStarting( info ); + } + void RunContext::benchmarkEnded( BenchmarkStats const& stats ) { + m_reporter->benchmarkEnded( stats ); + } + + void RunContext::pushScopedMessage(MessageInfo const & message) { + m_messages.push_back(message); + } + + void RunContext::popScopedMessage(MessageInfo const & message) { + m_messages.erase(std::remove(m_messages.begin(), m_messages.end(), message), m_messages.end()); + } + + std::string RunContext::getCurrentTestName() const { + return m_activeTestCase + ? m_activeTestCase->getTestCaseInfo().name + : std::string(); + } + + const AssertionResult * RunContext::getLastResult() const { + return &(*m_lastResult); + } + + void RunContext::exceptionEarlyReported() { + m_shouldReportUnexpected = false; + } + + void RunContext::handleFatalErrorCondition(std::string const & message) { + // Don't rebuild the result -- the stringification itself can cause more fatal errors + // Instead, fake a result data. + AssertionResultData tempResult( ResultWas::Unknown, { false } ); + tempResult.resultType = ResultWas::FatalErrorCondition; + tempResult.message = message; + AssertionResult result(m_lastAssertionInfo, tempResult); + + getResultCapture().assertionEnded(result); + + handleUnfinishedSections(); + + // Recreate section for test case (as we will lose the one that was in scope) + TestCaseInfo const& testCaseInfo = m_activeTestCase->getTestCaseInfo(); + SectionInfo testCaseSection(testCaseInfo.lineInfo, testCaseInfo.name, testCaseInfo.description); + + Counts assertions; + assertions.failed = 1; + SectionStats testCaseSectionStats(testCaseSection, assertions, 0, false); + m_reporter->sectionEnded(testCaseSectionStats); + + TestCaseInfo testInfo = m_activeTestCase->getTestCaseInfo(); + + Totals deltaTotals; + deltaTotals.testCases.failed = 1; + deltaTotals.assertions.failed = 1; + m_reporter->testCaseEnded(TestCaseStats(testInfo, + deltaTotals, + std::string(), + std::string(), + false)); + m_totals.testCases.failed++; + testGroupEnded(std::string(), m_totals, 1, 1); + m_reporter->testRunEnded(TestRunStats(m_runInfo, m_totals, false)); + } + + bool RunContext::lastAssertionPassed() { + return m_totals.assertions.passed == (m_prevPassed + 1); + } + + void RunContext::assertionPassed() { + ++m_totals.assertions.passed; + m_lastAssertionInfo.capturedExpression = "{Unknown expression after the reported line}"; + m_lastAssertionInfo.macroName = ""; + } + + void RunContext::assertionRun() { + m_prevPassed = m_totals.assertions.passed; + } + + bool RunContext::aborting() const { + return m_totals.assertions.failed == static_cast(m_config->abortAfter()); + } + + void RunContext::runCurrentTest(std::string & redirectedCout, std::string & redirectedCerr) { + TestCaseInfo const& testCaseInfo = m_activeTestCase->getTestCaseInfo(); + SectionInfo testCaseSection(testCaseInfo.lineInfo, testCaseInfo.name, testCaseInfo.description); + m_reporter->sectionStarting(testCaseSection); + Counts prevAssertions = m_totals.assertions; + double duration = 0; + m_shouldReportUnexpected = true; + try { + m_lastAssertionInfo = { "TEST_CASE", testCaseInfo.lineInfo, "", ResultDisposition::Normal }; + + seedRng(*m_config); + + Timer timer; + timer.start(); + if (m_reporter->getPreferences().shouldRedirectStdOut) { + StreamRedirect coutRedir(cout(), redirectedCout); + StdErrRedirect errRedir(redirectedCerr); + invokeActiveTestCase(); + } else { + invokeActiveTestCase(); + } + duration = timer.getElapsedSeconds(); + } catch (TestFailureException&) { + // This just means the test was aborted due to failure + } catch (...) { + // Under CATCH_CONFIG_FAST_COMPILE, unexpected exceptions under REQUIRE assertions + // are reported without translation at the point of origin. + if (m_shouldReportUnexpected) { + AssertionHandler + ( m_lastAssertionInfo.macroName, + m_lastAssertionInfo.lineInfo, + m_lastAssertionInfo.capturedExpression, + m_lastAssertionInfo.resultDisposition ).useActiveException(); + } + } + m_testCaseTracker->close(); + handleUnfinishedSections(); + m_messages.clear(); + + Counts assertions = m_totals.assertions - prevAssertions; + bool missingAssertions = testForMissingAssertions(assertions); + + if (testCaseInfo.okToFail()) { + std::swap(assertions.failedButOk, assertions.failed); + m_totals.assertions.failed -= assertions.failedButOk; + m_totals.assertions.failedButOk += assertions.failedButOk; + } + + SectionStats testCaseSectionStats(testCaseSection, assertions, duration, missingAssertions); + m_reporter->sectionEnded(testCaseSectionStats); + } + + void RunContext::invokeActiveTestCase() { + FatalConditionHandler fatalConditionHandler; // Handle signals + m_activeTestCase->invoke(); + fatalConditionHandler.reset(); + } + + void RunContext::handleUnfinishedSections() { + // If sections ended prematurely due to an exception we stored their + // infos here so we can tear them down outside the unwind process. + for (auto it = m_unfinishedSections.rbegin(), + itEnd = m_unfinishedSections.rend(); + it != itEnd; + ++it) + sectionEnded(*it); + m_unfinishedSections.clear(); + } + + IResultCapture& getResultCapture() { + if (IResultCapture* capture = getCurrentContext().getResultCapture()) + return *capture; + else + CATCH_INTERNAL_ERROR("No result capture instance"); + } +} +// end catch_run_context.cpp +// start catch_section.cpp + +namespace Catch { + + Section::Section( SectionInfo const& info ) + : m_info( info ), + m_sectionIncluded( getResultCapture().sectionStarted( m_info, m_assertions ) ) + { + m_timer.start(); + } + +#if defined(_MSC_VER) +#pragma warning(push) +#pragma warning(disable:4996) // std::uncaught_exception is deprecated in C++17 +#endif + Section::~Section() { + if( m_sectionIncluded ) { + SectionEndInfo endInfo( m_info, m_assertions, m_timer.getElapsedSeconds() ); + if( std::uncaught_exception() ) + getResultCapture().sectionEndedEarly( endInfo ); + else + getResultCapture().sectionEnded( endInfo ); + } + } +#if defined(_MSC_VER) +#pragma warning(pop) +#endif + + // This indicates whether the section should be executed or not + Section::operator bool() const { + return m_sectionIncluded; + } + +} // end namespace Catch +// end catch_section.cpp +// start catch_section_info.cpp + +namespace Catch { + + SectionInfo::SectionInfo + ( SourceLineInfo const& _lineInfo, + std::string const& _name, + std::string const& _description ) + : name( _name ), + description( _description ), + lineInfo( _lineInfo ) + {} + + SectionEndInfo::SectionEndInfo( SectionInfo const& _sectionInfo, Counts const& _prevAssertions, double _durationInSeconds ) + : sectionInfo( _sectionInfo ), prevAssertions( _prevAssertions ), durationInSeconds( _durationInSeconds ) + {} + +} // end namespace Catch +// end catch_section_info.cpp +// start catch_startup_exception_registry.cpp + +namespace Catch { + void StartupExceptionRegistry::add( std::exception_ptr const& exception ) noexcept { + try { + m_exceptions.push_back(exception); + } + catch(...) { + // If we run out of memory during start-up there's really not a lot more we can do about it + std::terminate(); + } + } + + std::vector const& StartupExceptionRegistry::getExceptions() const noexcept { + return m_exceptions; + } + +} // end namespace Catch +// end catch_startup_exception_registry.cpp +// start catch_stream.cpp + +#include +#include +#include + +namespace Catch { + + template + class StreamBufImpl : public StreamBufBase { + char data[bufferSize]; + WriterF m_writer; + + public: + StreamBufImpl() { + setp( data, data + sizeof(data) ); + } + + ~StreamBufImpl() noexcept { + StreamBufImpl::sync(); + } + + private: + int overflow( int c ) override { + sync(); + + if( c != EOF ) { + if( pbase() == epptr() ) + m_writer( std::string( 1, static_cast( c ) ) ); + else + sputc( static_cast( c ) ); + } + return 0; + } + + int sync() override { + if( pbase() != pptr() ) { + m_writer( std::string( pbase(), static_cast( pptr() - pbase() ) ) ); + setp( pbase(), epptr() ); + } + return 0; + } + }; + + /////////////////////////////////////////////////////////////////////////// + + FileStream::FileStream( std::string const& filename ) { + m_ofs.open( filename.c_str() ); + CATCH_ENFORCE( !m_ofs.fail(), "Unable to open file: '" << filename << "'" ); + } + + std::ostream& FileStream::stream() const { + return m_ofs; + } + + struct OutputDebugWriter { + + void operator()( std::string const&str ) { + writeToDebugConsole( str ); + } + }; + + DebugOutStream::DebugOutStream() + : m_streamBuf( new StreamBufImpl() ), + m_os( m_streamBuf.get() ) + {} + + std::ostream& DebugOutStream::stream() const { + return m_os; + } + + // Store the streambuf from cout up-front because + // cout may get redirected when running tests + CoutStream::CoutStream() + : m_os( Catch::cout().rdbuf() ) + {} + + std::ostream& CoutStream::stream() const { + return m_os; + } + +#ifndef CATCH_CONFIG_NOSTDOUT // If you #define this you must implement these functions + std::ostream& cout() { + return std::cout; + } + std::ostream& cerr() { + return std::cerr; + } + std::ostream& clog() { + return std::clog; + } +#endif +} +// end catch_stream.cpp +// start catch_string_manip.cpp + +#include +#include +#include +#include + +namespace Catch { + + bool startsWith( std::string const& s, std::string const& prefix ) { + return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin()); + } + bool startsWith( std::string const& s, char prefix ) { + return !s.empty() && s[0] == prefix; + } + bool endsWith( std::string const& s, std::string const& suffix ) { + return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin()); + } + bool endsWith( std::string const& s, char suffix ) { + return !s.empty() && s[s.size()-1] == suffix; + } + bool contains( std::string const& s, std::string const& infix ) { + return s.find( infix ) != std::string::npos; + } + char toLowerCh(char c) { + return static_cast( std::tolower( c ) ); + } + void toLowerInPlace( std::string& s ) { + std::transform( s.begin(), s.end(), s.begin(), toLowerCh ); + } + std::string toLower( std::string const& s ) { + std::string lc = s; + toLowerInPlace( lc ); + return lc; + } + std::string trim( std::string const& str ) { + static char const* whitespaceChars = "\n\r\t "; + std::string::size_type start = str.find_first_not_of( whitespaceChars ); + std::string::size_type end = str.find_last_not_of( whitespaceChars ); + + return start != std::string::npos ? str.substr( start, 1+end-start ) : std::string(); + } + + bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis ) { + bool replaced = false; + std::size_t i = str.find( replaceThis ); + while( i != std::string::npos ) { + replaced = true; + str = str.substr( 0, i ) + withThis + str.substr( i+replaceThis.size() ); + if( i < str.size()-withThis.size() ) + i = str.find( replaceThis, i+withThis.size() ); + else + i = std::string::npos; + } + return replaced; + } + + pluralise::pluralise( std::size_t count, std::string const& label ) + : m_count( count ), + m_label( label ) + {} + + std::ostream& operator << ( std::ostream& os, pluralise const& pluraliser ) { + os << pluraliser.m_count << ' ' << pluraliser.m_label; + if( pluraliser.m_count != 1 ) + os << 's'; + return os; + } + +} +// end catch_string_manip.cpp +// start catch_stringref.cpp + +#include +#include +#include + +namespace Catch { + + auto getEmptyStringRef() -> StringRef { + static StringRef s_emptyStringRef(""); + return s_emptyStringRef; + } + + StringRef::StringRef() noexcept + : StringRef( getEmptyStringRef() ) + {} + + StringRef::StringRef( StringRef const& other ) noexcept + : m_start( other.m_start ), + m_size( other.m_size ) + {} + + StringRef::StringRef( StringRef&& other ) noexcept + : m_start( other.m_start ), + m_size( other.m_size ), + m_data( other.m_data ) + { + other.m_data = nullptr; + } + + StringRef::StringRef( char const* rawChars ) noexcept + : m_start( rawChars ), + m_size( static_cast( std::strlen( rawChars ) ) ) + { + assert( rawChars != nullptr ); + } + + StringRef::StringRef( char const* rawChars, size_type size ) noexcept + : m_start( rawChars ), + m_size( size ) + { + size_type rawSize = rawChars == nullptr ? 0 : static_cast( std::strlen( rawChars ) ); + if( rawSize < size ) + m_size = rawSize; + } + + StringRef::StringRef( std::string const& stdString ) noexcept + : m_start( stdString.c_str() ), + m_size( stdString.size() ) + {} + + StringRef::~StringRef() noexcept { + delete[] m_data; + } + + auto StringRef::operator = ( StringRef other ) noexcept -> StringRef& { + swap( other ); + return *this; + } + StringRef::operator std::string() const { + return std::string( m_start, m_size ); + } + + void StringRef::swap( StringRef& other ) noexcept { + std::swap( m_start, other.m_start ); + std::swap( m_size, other.m_size ); + std::swap( m_data, other.m_data ); + } + + auto StringRef::c_str() const -> char const* { + if( isSubstring() ) + const_cast( this )->takeOwnership(); + return m_start; + } + auto StringRef::data() const noexcept -> char const* { + return m_start; + } + + auto StringRef::isOwned() const noexcept -> bool { + return m_data != nullptr; + } + auto StringRef::isSubstring() const noexcept -> bool { + return m_start[m_size] != '\0'; + } + + void StringRef::takeOwnership() { + if( !isOwned() ) { + m_data = new char[m_size+1]; + memcpy( m_data, m_start, m_size ); + m_data[m_size] = '\0'; + m_start = m_data; + } + } + auto StringRef::substr( size_type start, size_type size ) const noexcept -> StringRef { + if( start < m_size ) + return StringRef( m_start+start, size ); + else + return StringRef(); + } + auto StringRef::operator == ( StringRef const& other ) const noexcept -> bool { + return + size() == other.size() && + (std::strncmp( m_start, other.m_start, size() ) == 0); + } + auto StringRef::operator != ( StringRef const& other ) const noexcept -> bool { + return !operator==( other ); + } + + auto StringRef::operator[](size_type index) const noexcept -> char { + return m_start[index]; + } + + auto StringRef::empty() const noexcept -> bool { + return m_size == 0; + } + + auto StringRef::size() const noexcept -> size_type { + return m_size; + } + auto StringRef::numberOfCharacters() const noexcept -> size_type { + size_type noChars = m_size; + // Make adjustments for uft encodings + for( size_type i=0; i < m_size; ++i ) { + char c = m_start[i]; + if( ( c & 0b11000000 ) == 0b11000000 ) { + if( ( c & 0b11100000 ) == 0b11000000 ) + noChars--; + else if( ( c & 0b11110000 ) == 0b11100000 ) + noChars-=2; + else if( ( c & 0b11111000 ) == 0b11110000 ) + noChars-=3; + } + } + return noChars; + } + + auto operator + ( StringRef const& lhs, StringRef const& rhs ) -> std::string { + std::string str; + str.reserve( lhs.size() + rhs.size() ); + str += lhs; + str += rhs; + return str; + } + auto operator + ( StringRef const& lhs, const char* rhs ) -> std::string { + return std::string( lhs ) + std::string( rhs ); + } + auto operator + ( char const* lhs, StringRef const& rhs ) -> std::string { + return std::string( lhs ) + std::string( rhs ); + } + + auto operator << ( std::ostream& os, StringRef const& str ) -> std::ostream& { + return os << str.c_str(); + } + +} // namespace Catch +// end catch_stringref.cpp +// start catch_tag_alias.cpp + +namespace Catch { + TagAlias::TagAlias(std::string const & _tag, SourceLineInfo _lineInfo): tag(_tag), lineInfo(_lineInfo) {} +} +// end catch_tag_alias.cpp +// start catch_tag_alias_autoregistrar.cpp + +namespace Catch { + + RegistrarForTagAliases::RegistrarForTagAliases(char const* alias, char const* tag, SourceLineInfo const& lineInfo) { + try { + getMutableRegistryHub().registerTagAlias(alias, tag, lineInfo); + } catch (...) { + // Do not throw when constructing global objects, instead register the exception to be processed later + getMutableRegistryHub().registerStartupException(); + } + } + +} +// end catch_tag_alias_autoregistrar.cpp +// start catch_tag_alias_registry.cpp + +namespace Catch { + + TagAliasRegistry::~TagAliasRegistry() {} + + TagAlias const* TagAliasRegistry::find( std::string const& alias ) const { + auto it = m_registry.find( alias ); + if( it != m_registry.end() ) + return &(it->second); + else + return nullptr; + } + + std::string TagAliasRegistry::expandAliases( std::string const& unexpandedTestSpec ) const { + std::string expandedTestSpec = unexpandedTestSpec; + for( auto const& registryKvp : m_registry ) { + std::size_t pos = expandedTestSpec.find( registryKvp.first ); + if( pos != std::string::npos ) { + expandedTestSpec = expandedTestSpec.substr( 0, pos ) + + registryKvp.second.tag + + expandedTestSpec.substr( pos + registryKvp.first.size() ); + } + } + return expandedTestSpec; + } + + void TagAliasRegistry::add( std::string const& alias, std::string const& tag, SourceLineInfo const& lineInfo ) { + CATCH_ENFORCE( startsWith(alias, "[@") && endsWith(alias, ']'), + "error: tag alias, '" << alias << "' is not of the form [@alias name].\n" << lineInfo ); + + CATCH_ENFORCE( m_registry.insert(std::make_pair(alias, TagAlias(tag, lineInfo))).second, + "error: tag alias, '" << alias << "' already registered.\n" + << "\tFirst seen at: " << find(alias)->lineInfo << "\n" + << "\tRedefined at: " << lineInfo ); + } + + ITagAliasRegistry::~ITagAliasRegistry() {} + + ITagAliasRegistry const& ITagAliasRegistry::get() { + return getRegistryHub().getTagAliasRegistry(); + } + +} // end namespace Catch +// end catch_tag_alias_registry.cpp +// start catch_test_case_info.cpp + +#include +#include +#include + +namespace Catch { + + TestCaseInfo::SpecialProperties parseSpecialTag( std::string const& tag ) { + if( startsWith( tag, '.' ) || + tag == "hide" || + tag == "!hide" ) + return TestCaseInfo::IsHidden; + else if( tag == "!throws" ) + return TestCaseInfo::Throws; + else if( tag == "!shouldfail" ) + return TestCaseInfo::ShouldFail; + else if( tag == "!mayfail" ) + return TestCaseInfo::MayFail; + else if( tag == "!nonportable" ) + return TestCaseInfo::NonPortable; + else if( tag == "!benchmark" ) + return static_cast( TestCaseInfo::Benchmark | TestCaseInfo::IsHidden ); + else + return TestCaseInfo::None; + } + bool isReservedTag( std::string const& tag ) { + return parseSpecialTag( tag ) == TestCaseInfo::None && tag.size() > 0 && !std::isalnum( tag[0] ); + } + void enforceNotReservedTag( std::string const& tag, SourceLineInfo const& _lineInfo ) { + CATCH_ENFORCE( !isReservedTag(tag), + "Tag name: [" << tag << "] is not allowed.\n" + << "Tag names starting with non alpha-numeric characters are reserved\n" + << _lineInfo ); + } + + TestCase makeTestCase( ITestInvoker* _testCase, + std::string const& _className, + std::string const& _name, + std::string const& _descOrTags, + SourceLineInfo const& _lineInfo ) + { + bool isHidden( startsWith( _name, "./" ) ); // Legacy support + + // Parse out tags + std::vector tags; + std::string desc, tag; + bool inTag = false; + for( std::size_t i = 0; i < _descOrTags.size(); ++i ) { + char c = _descOrTags[i]; + if( !inTag ) { + if( c == '[' ) + inTag = true; + else + desc += c; + } + else { + if( c == ']' ) { + TestCaseInfo::SpecialProperties prop = parseSpecialTag( tag ); + if( ( prop & TestCaseInfo::IsHidden ) != 0 ) + isHidden = true; + else if( prop == TestCaseInfo::None ) + enforceNotReservedTag( tag, _lineInfo ); + + tags.push_back( tag ); + tag.clear(); + inTag = false; + } + else + tag += c; + } + } + if( isHidden ) { + tags.push_back( "hide" ); + tags.push_back( "." ); + } + + TestCaseInfo info( _name, _className, desc, tags, _lineInfo ); + return TestCase( _testCase, info ); + } + + void setTags( TestCaseInfo& testCaseInfo, std::vector tags ) { + std::sort(begin(tags), end(tags)); + tags.erase(std::unique(begin(tags), end(tags)), end(tags)); + testCaseInfo.lcaseTags.clear(); + + for( auto const& tag : tags ) { + std::string lcaseTag = toLower( tag ); + testCaseInfo.properties = static_cast( testCaseInfo.properties | parseSpecialTag( lcaseTag ) ); + testCaseInfo.lcaseTags.push_back( lcaseTag ); + } + testCaseInfo.tags = std::move(tags); + } + + TestCaseInfo::TestCaseInfo( std::string const& _name, + std::string const& _className, + std::string const& _description, + std::vector const& _tags, + SourceLineInfo const& _lineInfo ) + : name( _name ), + className( _className ), + description( _description ), + lineInfo( _lineInfo ), + properties( None ) + { + setTags( *this, _tags ); + } + + bool TestCaseInfo::isHidden() const { + return ( properties & IsHidden ) != 0; + } + bool TestCaseInfo::throws() const { + return ( properties & Throws ) != 0; + } + bool TestCaseInfo::okToFail() const { + return ( properties & (ShouldFail | MayFail ) ) != 0; + } + bool TestCaseInfo::expectedToFail() const { + return ( properties & (ShouldFail ) ) != 0; + } + + std::string TestCaseInfo::tagsAsString() const { + std::string ret; + // '[' and ']' per tag + size_t full_size = 2 * tags.size(); + for (const auto& tag : tags) { + full_size += tag.size(); + } + ret.reserve(full_size); + for (const auto& tag : tags) { + ret.push_back('['); + ret.append(tag); + ret.push_back(']'); + } + + return ret; + } + + TestCase::TestCase( ITestInvoker* testCase, TestCaseInfo const& info ) : TestCaseInfo( info ), test( testCase ) {} + + TestCase TestCase::withName( std::string const& _newName ) const { + TestCase other( *this ); + other.name = _newName; + return other; + } + + void TestCase::invoke() const { + test->invoke(); + } + + bool TestCase::operator == ( TestCase const& other ) const { + return test.get() == other.test.get() && + name == other.name && + className == other.className; + } + + bool TestCase::operator < ( TestCase const& other ) const { + return name < other.name; + } + + TestCaseInfo const& TestCase::getTestCaseInfo() const + { + return *this; + } + +} // end namespace Catch +// end catch_test_case_info.cpp +// start catch_test_case_registry_impl.cpp + +#include + +namespace Catch { + + RandomNumberGenerator::result_type RandomNumberGenerator::operator()( result_type n ) const { return std::rand() % n; } + RandomNumberGenerator::result_type RandomNumberGenerator::operator()() const { return std::rand() % max(); } + + std::vector sortTests( IConfig const& config, std::vector const& unsortedTestCases ) { + + std::vector sorted = unsortedTestCases; + + switch( config.runOrder() ) { + case RunTests::InLexicographicalOrder: + std::sort( sorted.begin(), sorted.end() ); + break; + case RunTests::InRandomOrder: + seedRng( config ); + RandomNumberGenerator::shuffle( sorted ); + break; + case RunTests::InDeclarationOrder: + // already in declaration order + break; + } + return sorted; + } + bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ) { + return testSpec.matches( testCase ) && ( config.allowThrows() || !testCase.throws() ); + } + + void enforceNoDuplicateTestCases( std::vector const& functions ) { + std::set seenFunctions; + for( auto const& function : functions ) { + auto prev = seenFunctions.insert( function ); + CATCH_ENFORCE( prev.second, + "error: TEST_CASE( \"" << function.name << "\" ) already defined.\n" + << "\tFirst seen at " << prev.first->getTestCaseInfo().lineInfo << "\n" + << "\tRedefined at " << function.getTestCaseInfo().lineInfo ); + } + } + + std::vector filterTests( std::vector const& testCases, TestSpec const& testSpec, IConfig const& config ) { + std::vector filtered; + filtered.reserve( testCases.size() ); + for( auto const& testCase : testCases ) + if( matchTest( testCase, testSpec, config ) ) + filtered.push_back( testCase ); + return filtered; + } + std::vector const& getAllTestCasesSorted( IConfig const& config ) { + return getRegistryHub().getTestCaseRegistry().getAllTestsSorted( config ); + } + + void TestRegistry::registerTest( TestCase const& testCase ) { + std::string name = testCase.getTestCaseInfo().name; + if( name.empty() ) { + std::ostringstream oss; + oss << "Anonymous test case " << ++m_unnamedCount; + return registerTest( testCase.withName( oss.str() ) ); + } + m_functions.push_back( testCase ); + } + + std::vector const& TestRegistry::getAllTests() const { + return m_functions; + } + std::vector const& TestRegistry::getAllTestsSorted( IConfig const& config ) const { + if( m_sortedFunctions.empty() ) + enforceNoDuplicateTestCases( m_functions ); + + if( m_currentSortOrder != config.runOrder() || m_sortedFunctions.empty() ) { + m_sortedFunctions = sortTests( config, m_functions ); + m_currentSortOrder = config.runOrder(); + } + return m_sortedFunctions; + } + + /////////////////////////////////////////////////////////////////////////// + TestInvokerAsFunction::TestInvokerAsFunction( void(*testAsFunction)() ) noexcept : m_testAsFunction( testAsFunction ) {} + + void TestInvokerAsFunction::invoke() const { + m_testAsFunction(); + } + + std::string extractClassName( std::string const& classOrQualifiedMethodName ) { + std::string className = classOrQualifiedMethodName; + if( startsWith( className, '&' ) ) + { + std::size_t lastColons = className.rfind( "::" ); + std::size_t penultimateColons = className.rfind( "::", lastColons-1 ); + if( penultimateColons == std::string::npos ) + penultimateColons = 1; + className = className.substr( penultimateColons, lastColons-penultimateColons ); + } + return className; + } + +} // end namespace Catch +// end catch_test_case_registry_impl.cpp +// start catch_test_case_tracker.cpp + +#include +#include +#include +#include + +CATCH_INTERNAL_SUPPRESS_ETD_WARNINGS + +namespace Catch { +namespace TestCaseTracking { + + NameAndLocation::NameAndLocation( std::string const& _name, SourceLineInfo const& _location ) + : name( _name ), + location( _location ) + {} + + TrackerContext& TrackerContext::instance() { + static TrackerContext s_instance; + return s_instance; + } + + ITracker& TrackerContext::startRun() { + m_rootTracker = std::make_shared( NameAndLocation( "{root}", CATCH_INTERNAL_LINEINFO ), *this, nullptr ); + m_currentTracker = nullptr; + m_runState = Executing; + return *m_rootTracker; + } + + void TrackerContext::endRun() { + m_rootTracker.reset(); + m_currentTracker = nullptr; + m_runState = NotStarted; + } + + void TrackerContext::startCycle() { + m_currentTracker = m_rootTracker.get(); + m_runState = Executing; + } + void TrackerContext::completeCycle() { + m_runState = CompletedCycle; + } + + bool TrackerContext::completedCycle() const { + return m_runState == CompletedCycle; + } + ITracker& TrackerContext::currentTracker() { + return *m_currentTracker; + } + void TrackerContext::setCurrentTracker( ITracker* tracker ) { + m_currentTracker = tracker; + } + + TrackerBase::TrackerHasName::TrackerHasName( NameAndLocation const& nameAndLocation ) : m_nameAndLocation( nameAndLocation ) {} + bool TrackerBase::TrackerHasName::operator ()( ITrackerPtr const& tracker ) const { + return + tracker->nameAndLocation().name == m_nameAndLocation.name && + tracker->nameAndLocation().location == m_nameAndLocation.location; + } + + TrackerBase::TrackerBase( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ) + : m_nameAndLocation( nameAndLocation ), + m_ctx( ctx ), + m_parent( parent ) + {} + + NameAndLocation const& TrackerBase::nameAndLocation() const { + return m_nameAndLocation; + } + bool TrackerBase::isComplete() const { + return m_runState == CompletedSuccessfully || m_runState == Failed; + } + bool TrackerBase::isSuccessfullyCompleted() const { + return m_runState == CompletedSuccessfully; + } + bool TrackerBase::isOpen() const { + return m_runState != NotStarted && !isComplete(); + } + bool TrackerBase::hasChildren() const { + return !m_children.empty(); + } + + void TrackerBase::addChild( ITrackerPtr const& child ) { + m_children.push_back( child ); + } + + ITrackerPtr TrackerBase::findChild( NameAndLocation const& nameAndLocation ) { + auto it = std::find_if( m_children.begin(), m_children.end(), TrackerHasName( nameAndLocation ) ); + return( it != m_children.end() ) + ? *it + : nullptr; + } + ITracker& TrackerBase::parent() { + assert( m_parent ); // Should always be non-null except for root + return *m_parent; + } + + void TrackerBase::openChild() { + if( m_runState != ExecutingChildren ) { + m_runState = ExecutingChildren; + if( m_parent ) + m_parent->openChild(); + } + } + + bool TrackerBase::isSectionTracker() const { return false; } + bool TrackerBase::isIndexTracker() const { return false; } + + void TrackerBase::open() { + m_runState = Executing; + moveToThis(); + if( m_parent ) + m_parent->openChild(); + } + + void TrackerBase::close() { + + // Close any still open children (e.g. generators) + while( &m_ctx.currentTracker() != this ) + m_ctx.currentTracker().close(); + + switch( m_runState ) { + case NeedsAnotherRun: + break; + + case Executing: + m_runState = CompletedSuccessfully; + break; + case ExecutingChildren: + if( m_children.empty() || m_children.back()->isComplete() ) + m_runState = CompletedSuccessfully; + break; + + case NotStarted: + case CompletedSuccessfully: + case Failed: + CATCH_INTERNAL_ERROR( "Illogical state: " << m_runState ); + + default: + CATCH_INTERNAL_ERROR( "Unknown state: " << m_runState ); + } + moveToParent(); + m_ctx.completeCycle(); + } + void TrackerBase::fail() { + m_runState = Failed; + if( m_parent ) + m_parent->markAsNeedingAnotherRun(); + moveToParent(); + m_ctx.completeCycle(); + } + void TrackerBase::markAsNeedingAnotherRun() { + m_runState = NeedsAnotherRun; + } + + void TrackerBase::moveToParent() { + assert( m_parent ); + m_ctx.setCurrentTracker( m_parent ); + } + void TrackerBase::moveToThis() { + m_ctx.setCurrentTracker( this ); + } + + SectionTracker::SectionTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent ) + : TrackerBase( nameAndLocation, ctx, parent ) + { + if( parent ) { + while( !parent->isSectionTracker() ) + parent = &parent->parent(); + + SectionTracker& parentSection = static_cast( *parent ); + addNextFilters( parentSection.m_filters ); + } + } + + bool SectionTracker::isSectionTracker() const { return true; } + + SectionTracker& SectionTracker::acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation ) { + std::shared_ptr section; + + ITracker& currentTracker = ctx.currentTracker(); + if( ITrackerPtr childTracker = currentTracker.findChild( nameAndLocation ) ) { + assert( childTracker ); + assert( childTracker->isSectionTracker() ); + section = std::static_pointer_cast( childTracker ); + } + else { + section = std::make_shared( nameAndLocation, ctx, ¤tTracker ); + currentTracker.addChild( section ); + } + if( !ctx.completedCycle() ) + section->tryOpen(); + return *section; + } + + void SectionTracker::tryOpen() { + if( !isComplete() && (m_filters.empty() || m_filters[0].empty() || m_filters[0] == m_nameAndLocation.name ) ) + open(); + } + + void SectionTracker::addInitialFilters( std::vector const& filters ) { + if( !filters.empty() ) { + m_filters.push_back(""); // Root - should never be consulted + m_filters.push_back(""); // Test Case - not a section filter + m_filters.insert( m_filters.end(), filters.begin(), filters.end() ); + } + } + void SectionTracker::addNextFilters( std::vector const& filters ) { + if( filters.size() > 1 ) + m_filters.insert( m_filters.end(), ++filters.begin(), filters.end() ); + } + + IndexTracker::IndexTracker( NameAndLocation const& nameAndLocation, TrackerContext& ctx, ITracker* parent, int size ) + : TrackerBase( nameAndLocation, ctx, parent ), + m_size( size ) + {} + + bool IndexTracker::isIndexTracker() const { return true; } + + IndexTracker& IndexTracker::acquire( TrackerContext& ctx, NameAndLocation const& nameAndLocation, int size ) { + std::shared_ptr tracker; + + ITracker& currentTracker = ctx.currentTracker(); + if( ITrackerPtr childTracker = currentTracker.findChild( nameAndLocation ) ) { + assert( childTracker ); + assert( childTracker->isIndexTracker() ); + tracker = std::static_pointer_cast( childTracker ); + } + else { + tracker = std::make_shared( nameAndLocation, ctx, ¤tTracker, size ); + currentTracker.addChild( tracker ); + } + + if( !ctx.completedCycle() && !tracker->isComplete() ) { + if( tracker->m_runState != ExecutingChildren && tracker->m_runState != NeedsAnotherRun ) + tracker->moveNext(); + tracker->open(); + } + + return *tracker; + } + + int IndexTracker::index() const { return m_index; } + + void IndexTracker::moveNext() { + m_index++; + m_children.clear(); + } + + void IndexTracker::close() { + TrackerBase::close(); + if( m_runState == CompletedSuccessfully && m_index < m_size-1 ) + m_runState = Executing; + } + +} // namespace TestCaseTracking + +using TestCaseTracking::ITracker; +using TestCaseTracking::TrackerContext; +using TestCaseTracking::SectionTracker; +using TestCaseTracking::IndexTracker; + +} // namespace Catch + +CATCH_INTERNAL_UNSUPPRESS_ETD_WARNINGS +// end catch_test_case_tracker.cpp +// start catch_test_registry.cpp + +namespace Catch { + + auto makeTestInvoker( void(*testAsFunction)() ) noexcept -> ITestInvoker* { + return new(std::nothrow) TestInvokerAsFunction( testAsFunction ); + } + + NameAndTags::NameAndTags( StringRef name_ , StringRef tags_ ) noexcept : name( name_ ), tags( tags_ ) {} + + AutoReg::AutoReg( ITestInvoker* invoker, SourceLineInfo const& lineInfo, StringRef classOrMethod, NameAndTags const& nameAndTags ) noexcept { + try { + getMutableRegistryHub() + .registerTest( + makeTestCase( + invoker, + extractClassName( classOrMethod ), + nameAndTags.name, + nameAndTags.tags, + lineInfo)); + } catch (...) { + // Do not throw when constructing global objects, instead register the exception to be processed later + getMutableRegistryHub().registerStartupException(); + } + } +} +// end catch_test_registry.cpp +// start catch_test_spec.cpp + +#include +#include +#include +#include + +namespace Catch { + + TestSpec::NamePattern::NamePattern( std::string const& name ) + : m_wildcardPattern( toLower( name ), CaseSensitive::No ) + {} + bool TestSpec::NamePattern::matches( TestCaseInfo const& testCase ) const { + return m_wildcardPattern.matches( toLower( testCase.name ) ); + } + + TestSpec::TagPattern::TagPattern( std::string const& tag ) : m_tag( toLower( tag ) ) {} + bool TestSpec::TagPattern::matches( TestCaseInfo const& testCase ) const { + return std::find(begin(testCase.lcaseTags), + end(testCase.lcaseTags), + m_tag) != end(testCase.lcaseTags); + } + + TestSpec::ExcludedPattern::ExcludedPattern( PatternPtr const& underlyingPattern ) : m_underlyingPattern( underlyingPattern ) {} + bool TestSpec::ExcludedPattern::matches( TestCaseInfo const& testCase ) const { return !m_underlyingPattern->matches( testCase ); } + + bool TestSpec::Filter::matches( TestCaseInfo const& testCase ) const { + // All patterns in a filter must match for the filter to be a match + for( auto const& pattern : m_patterns ) { + if( !pattern->matches( testCase ) ) + return false; + } + return true; + } + + bool TestSpec::hasFilters() const { + return !m_filters.empty(); + } + bool TestSpec::matches( TestCaseInfo const& testCase ) const { + // A TestSpec matches if any filter matches + for( auto const& filter : m_filters ) + if( filter.matches( testCase ) ) + return true; + return false; + } +} +// end catch_test_spec.cpp +// start catch_test_spec_parser.cpp + +namespace Catch { + + TestSpecParser::TestSpecParser( ITagAliasRegistry const& tagAliases ) : m_tagAliases( &tagAliases ) {} + + TestSpecParser& TestSpecParser::parse( std::string const& arg ) { + m_mode = None; + m_exclusion = false; + m_start = std::string::npos; + m_arg = m_tagAliases->expandAliases( arg ); + m_escapeChars.clear(); + for( m_pos = 0; m_pos < m_arg.size(); ++m_pos ) + visitChar( m_arg[m_pos] ); + if( m_mode == Name ) + addPattern(); + return *this; + } + TestSpec TestSpecParser::testSpec() { + addFilter(); + return m_testSpec; + } + + void TestSpecParser::visitChar( char c ) { + if( m_mode == None ) { + switch( c ) { + case ' ': return; + case '~': m_exclusion = true; return; + case '[': return startNewMode( Tag, ++m_pos ); + case '"': return startNewMode( QuotedName, ++m_pos ); + case '\\': return escape(); + default: startNewMode( Name, m_pos ); break; + } + } + if( m_mode == Name ) { + if( c == ',' ) { + addPattern(); + addFilter(); + } + else if( c == '[' ) { + if( subString() == "exclude:" ) + m_exclusion = true; + else + addPattern(); + startNewMode( Tag, ++m_pos ); + } + else if( c == '\\' ) + escape(); + } + else if( m_mode == EscapedName ) + m_mode = Name; + else if( m_mode == QuotedName && c == '"' ) + addPattern(); + else if( m_mode == Tag && c == ']' ) + addPattern(); + } + void TestSpecParser::startNewMode( Mode mode, std::size_t start ) { + m_mode = mode; + m_start = start; + } + void TestSpecParser::escape() { + if( m_mode == None ) + m_start = m_pos; + m_mode = EscapedName; + m_escapeChars.push_back( m_pos ); + } + std::string TestSpecParser::subString() const { return m_arg.substr( m_start, m_pos - m_start ); } + + void TestSpecParser::addFilter() { + if( !m_currentFilter.m_patterns.empty() ) { + m_testSpec.m_filters.push_back( m_currentFilter ); + m_currentFilter = TestSpec::Filter(); + } + } + + TestSpec parseTestSpec( std::string const& arg ) { + return TestSpecParser( ITagAliasRegistry::get() ).parse( arg ).testSpec(); + } + +} // namespace Catch +// end catch_test_spec_parser.cpp +// start catch_timer.cpp + +#include + +namespace Catch { + + auto getCurrentNanosecondsSinceEpoch() -> uint64_t { + return std::chrono::duration_cast( std::chrono::high_resolution_clock::now().time_since_epoch() ).count(); + } + + auto estimateClockResolution() -> uint64_t { + uint64_t sum = 0; + static const uint64_t iterations = 1000000; + + for( size_t i = 0; i < iterations; ++i ) { + + uint64_t ticks; + uint64_t baseTicks = getCurrentNanosecondsSinceEpoch(); + do { + ticks = getCurrentNanosecondsSinceEpoch(); + } + while( ticks == baseTicks ); + + auto delta = ticks - baseTicks; + sum += delta; + } + + // We're just taking the mean, here. To do better we could take the std. dev and exclude outliers + // - and potentially do more iterations if there's a high variance. + return sum/iterations; + } + auto getEstimatedClockResolution() -> uint64_t { + static auto s_resolution = estimateClockResolution(); + return s_resolution; + } + + void Timer::start() { + m_nanoseconds = getCurrentNanosecondsSinceEpoch(); + } + auto Timer::getElapsedNanoseconds() const -> unsigned int { + return static_cast(getCurrentNanosecondsSinceEpoch() - m_nanoseconds); + } + auto Timer::getElapsedMicroseconds() const -> unsigned int { + return static_cast(getElapsedNanoseconds()/1000); + } + auto Timer::getElapsedMilliseconds() const -> unsigned int { + return static_cast(getElapsedMicroseconds()/1000); + } + auto Timer::getElapsedSeconds() const -> double { + return getElapsedMicroseconds()/1000000.0; + } + +} // namespace Catch +// end catch_timer.cpp +// start catch_tostring.cpp + +#include + +namespace Catch { + +namespace Detail { + + const std::string unprintableString = "{?}"; + + namespace { + const int hexThreshold = 255; + + struct Endianness { + enum Arch { Big, Little }; + + static Arch which() { + union _{ + int asInt; + char asChar[sizeof (int)]; + } u; + + u.asInt = 1; + return ( u.asChar[sizeof(int)-1] == 1 ) ? Big : Little; + } + }; + } + + std::string rawMemoryToString( const void *object, std::size_t size ) { + // Reverse order for little endian architectures + int i = 0, end = static_cast( size ), inc = 1; + if( Endianness::which() == Endianness::Little ) { + i = end-1; + end = inc = -1; + } + + unsigned char const *bytes = static_cast(object); + std::ostringstream os; + os << "0x" << std::setfill('0') << std::hex; + for( ; i != end; i += inc ) + os << std::setw(2) << static_cast(bytes[i]); + return os.str(); + } +} + +template +std::string fpToString( T value, int precision ) { + std::ostringstream oss; + oss << std::setprecision( precision ) + << std::fixed + << value; + std::string d = oss.str(); + std::size_t i = d.find_last_not_of( '0' ); + if( i != std::string::npos && i != d.size()-1 ) { + if( d[i] == '.' ) + i++; + d = d.substr( 0, i+1 ); + } + return d; +} + +//// ======================================================= //// +// +// Out-of-line defs for full specialization of StringMaker +// +//// ======================================================= //// + +std::string StringMaker::convert(const std::string& str) { + if (!getCurrentContext().getConfig()->showInvisibles()) { + return '"' + str + '"'; + } + + std::string s("\""); + for (char c : str) { + switch (c) { + case '\n': + s.append("\\n"); + break; + case '\t': + s.append("\\t"); + break; + default: + s.push_back(c); + break; + } + } + s.append("\""); + return s; +} + +std::string StringMaker::convert(const std::wstring& wstr) { + std::string s; + s.reserve(wstr.size()); + for (auto c : wstr) { + s += (c <= 0xff) ? static_cast(c) : '?'; + } + return ::Catch::Detail::stringify(s); +} + +std::string StringMaker::convert(char const* str) { + if (str) { + return ::Catch::Detail::stringify(std::string{ str }); + } else { + return{ "{null string}" }; + } +} +std::string StringMaker::convert(char* str) { + if (str) { + return ::Catch::Detail::stringify(std::string{ str }); + } else { + return{ "{null string}" }; + } +} +std::string StringMaker::convert(wchar_t const * str) { + if (str) { + return ::Catch::Detail::stringify(std::wstring{ str }); + } else { + return{ "{null string}" }; + } +} +std::string StringMaker::convert(wchar_t * str) { + if (str) { + return ::Catch::Detail::stringify(std::wstring{ str }); + } else { + return{ "{null string}" }; + } +} + +std::string StringMaker::convert(int value) { + return ::Catch::Detail::stringify(static_cast(value)); +} +std::string StringMaker::convert(long value) { + return ::Catch::Detail::stringify(static_cast(value)); +} +std::string StringMaker::convert(long long value) { + std::ostringstream oss; + oss << value; + if (value > Detail::hexThreshold) { + oss << " (0x" << std::hex << value << ')'; + } + return oss.str(); +} + +std::string StringMaker::convert(unsigned int value) { + return ::Catch::Detail::stringify(static_cast(value)); +} +std::string StringMaker::convert(unsigned long value) { + return ::Catch::Detail::stringify(static_cast(value)); +} +std::string StringMaker::convert(unsigned long long value) { + std::ostringstream oss; + oss << value; + if (value > Detail::hexThreshold) { + oss << " (0x" << std::hex << value << ')'; + } + return oss.str(); +} + +std::string StringMaker::convert(bool b) { + return b ? "true" : "false"; +} + +std::string StringMaker::convert(char value) { + if (value == '\r') { + return "'\\r'"; + } else if (value == '\f') { + return "'\\f'"; + } else if (value == '\n') { + return "'\\n'"; + } else if (value == '\t') { + return "'\\t'"; + } else if ('\0' <= value && value < ' ') { + return ::Catch::Detail::stringify(static_cast(value)); + } else { + char chstr[] = "' '"; + chstr[1] = value; + return chstr; + } +} +std::string StringMaker::convert(signed char c) { + return ::Catch::Detail::stringify(static_cast(c)); +} +std::string StringMaker::convert(unsigned char c) { + return ::Catch::Detail::stringify(static_cast(c)); +} + +std::string StringMaker::convert(std::nullptr_t) { + return "nullptr"; +} + +std::string StringMaker::convert(float value) { + return fpToString(value, 5) + 'f'; +} +std::string StringMaker::convert(double value) { + return fpToString(value, 10); +} + +#ifdef __OBJC__ +std::string StringMaker::convert(NSString* nsstring) { + if (!nsstring) + return "nil"; + return "@" + toString([nsstring UTF8String]); +} +std::string StringMaker::convert(NSString* CATCH_ARC_STRONG nsstring) { + if (!nsstring) + return "nil"; + return "@" + toString([nsstring UTF8String]); +} +std::string StringMaker::convert(NSObject* nsObject) { + return ::Catch::Detail::stringify([nsObject description]); +} +#endif + +} // end namespace Catch +// end catch_tostring.cpp +// start catch_totals.cpp + +namespace Catch { + + Counts Counts::operator - ( Counts const& other ) const { + Counts diff; + diff.passed = passed - other.passed; + diff.failed = failed - other.failed; + diff.failedButOk = failedButOk - other.failedButOk; + return diff; + } + + Counts& Counts::operator += ( Counts const& other ) { + passed += other.passed; + failed += other.failed; + failedButOk += other.failedButOk; + return *this; + } + + std::size_t Counts::total() const { + return passed + failed + failedButOk; + } + bool Counts::allPassed() const { + return failed == 0 && failedButOk == 0; + } + bool Counts::allOk() const { + return failed == 0; + } + + Totals Totals::operator - ( Totals const& other ) const { + Totals diff; + diff.assertions = assertions - other.assertions; + diff.testCases = testCases - other.testCases; + return diff; + } + + Totals& Totals::operator += ( Totals const& other ) { + assertions += other.assertions; + testCases += other.testCases; + return *this; + } + + Totals Totals::delta( Totals const& prevTotals ) const { + Totals diff = *this - prevTotals; + if( diff.assertions.failed > 0 ) + ++diff.testCases.failed; + else if( diff.assertions.failedButOk > 0 ) + ++diff.testCases.failedButOk; + else + ++diff.testCases.passed; + return diff; + } + +} +// end catch_totals.cpp +// start catch_version.cpp + +#include + +namespace Catch { + + Version::Version + ( unsigned int _majorVersion, + unsigned int _minorVersion, + unsigned int _patchNumber, + char const * const _branchName, + unsigned int _buildNumber ) + : majorVersion( _majorVersion ), + minorVersion( _minorVersion ), + patchNumber( _patchNumber ), + branchName( _branchName ), + buildNumber( _buildNumber ) + {} + + std::ostream& operator << ( std::ostream& os, Version const& version ) { + os << version.majorVersion << '.' + << version.minorVersion << '.' + << version.patchNumber; + // branchName is never null -> 0th char is \0 if it is empty + if (version.branchName[0]) { + os << '-' << version.branchName + << '.' << version.buildNumber; + } + return os; + } + + Version const& libraryVersion() { + static Version version( 2, 0, 0, "develop", 2 ); + return version; + } + +} +// end catch_version.cpp +// start catch_wildcard_pattern.cpp + +namespace Catch { + + WildcardPattern::WildcardPattern( std::string const& pattern, + CaseSensitive::Choice caseSensitivity ) + : m_caseSensitivity( caseSensitivity ), + m_pattern( adjustCase( pattern ) ) + { + if( startsWith( m_pattern, '*' ) ) { + m_pattern = m_pattern.substr( 1 ); + m_wildcard = WildcardAtStart; + } + if( endsWith( m_pattern, '*' ) ) { + m_pattern = m_pattern.substr( 0, m_pattern.size()-1 ); + m_wildcard = static_cast( m_wildcard | WildcardAtEnd ); + } + } + + bool WildcardPattern::matches( std::string const& str ) const { + switch( m_wildcard ) { + case NoWildcard: + return m_pattern == adjustCase( str ); + case WildcardAtStart: + return endsWith( adjustCase( str ), m_pattern ); + case WildcardAtEnd: + return startsWith( adjustCase( str ), m_pattern ); + case WildcardAtBothEnds: + return contains( adjustCase( str ), m_pattern ); + default: + CATCH_INTERNAL_ERROR( "Unknown enum" ); + } + } + + std::string WildcardPattern::adjustCase( std::string const& str ) const { + return m_caseSensitivity == CaseSensitive::No ? toLower( str ) : str; + } +} +// end catch_wildcard_pattern.cpp +// start catch_xmlwriter.cpp + +// start catch_xmlwriter.hpp + +#include +#include + +namespace Catch { + + class XmlEncode { + public: + enum ForWhat { ForTextNodes, ForAttributes }; + + XmlEncode( std::string const& str, ForWhat forWhat = ForTextNodes ); + + void encodeTo( std::ostream& os ) const; + + friend std::ostream& operator << ( std::ostream& os, XmlEncode const& xmlEncode ); + + private: + std::string m_str; + ForWhat m_forWhat; + }; + + class XmlWriter { + public: + + class ScopedElement { + public: + ScopedElement( XmlWriter* writer ); + + ScopedElement( ScopedElement&& other ) noexcept; + ScopedElement& operator=( ScopedElement&& other ) noexcept; + + ~ScopedElement(); + + ScopedElement& writeText( std::string const& text, bool indent = true ); + + template + ScopedElement& writeAttribute( std::string const& name, T const& attribute ) { + m_writer->writeAttribute( name, attribute ); + return *this; + } + + private: + mutable XmlWriter* m_writer = nullptr; + }; + + XmlWriter( std::ostream& os = Catch::cout() ); + ~XmlWriter(); + + XmlWriter( XmlWriter const& ) = delete; + XmlWriter& operator=( XmlWriter const& ) = delete; + + XmlWriter& startElement( std::string const& name ); + + ScopedElement scopedElement( std::string const& name ); + + XmlWriter& endElement(); + + XmlWriter& writeAttribute( std::string const& name, std::string const& attribute ); + + XmlWriter& writeAttribute( std::string const& name, bool attribute ); + + template + XmlWriter& writeAttribute( std::string const& name, T const& attribute ) { + m_oss.clear(); + m_oss.str(std::string()); + m_oss << attribute; + return writeAttribute( name, m_oss.str() ); + } + + XmlWriter& writeText( std::string const& text, bool indent = true ); + + XmlWriter& writeComment( std::string const& text ); + + void writeStylesheetRef( std::string const& url ); + + XmlWriter& writeBlankLine(); + + void ensureTagClosed(); + + private: + + void writeDeclaration(); + + void newlineIfNecessary(); + + bool m_tagIsOpen = false; + bool m_needsNewline = false; + std::vector m_tags; + std::string m_indent; + std::ostream& m_os; + std::ostringstream m_oss; + }; + +} + +// end catch_xmlwriter.hpp +#include + +namespace Catch { + + XmlEncode::XmlEncode( std::string const& str, ForWhat forWhat ) + : m_str( str ), + m_forWhat( forWhat ) + {} + + void XmlEncode::encodeTo( std::ostream& os ) const { + + // Apostrophe escaping not necessary if we always use " to write attributes + // (see: http://www.w3.org/TR/xml/#syntax) + + for( std::size_t i = 0; i < m_str.size(); ++ i ) { + char c = m_str[i]; + switch( c ) { + case '<': os << "<"; break; + case '&': os << "&"; break; + + case '>': + // See: http://www.w3.org/TR/xml/#syntax + if( i > 2 && m_str[i-1] == ']' && m_str[i-2] == ']' ) + os << ">"; + else + os << c; + break; + + case '\"': + if( m_forWhat == ForAttributes ) + os << """; + else + os << c; + break; + + default: + // Escape control chars - based on contribution by @espenalb in PR #465 and + // by @mrpi PR #588 + if ( ( c >= 0 && c < '\x09' ) || ( c > '\x0D' && c < '\x20') || c=='\x7F' ) { + // see http://stackoverflow.com/questions/404107/why-are-control-characters-illegal-in-xml-1-0 + os << "\\x" << std::uppercase << std::hex << std::setfill('0') << std::setw(2) + << static_cast( c ); + } + else + os << c; + } + } + } + + std::ostream& operator << ( std::ostream& os, XmlEncode const& xmlEncode ) { + xmlEncode.encodeTo( os ); + return os; + } + + XmlWriter::ScopedElement::ScopedElement( XmlWriter* writer ) + : m_writer( writer ) + {} + + XmlWriter::ScopedElement::ScopedElement( ScopedElement&& other ) noexcept + : m_writer( other.m_writer ){ + other.m_writer = nullptr; + } + XmlWriter::ScopedElement& XmlWriter::ScopedElement::operator=( ScopedElement&& other ) noexcept { + if ( m_writer ) { + m_writer->endElement(); + } + m_writer = other.m_writer; + other.m_writer = nullptr; + return *this; + } + + XmlWriter::ScopedElement::~ScopedElement() { + if( m_writer ) + m_writer->endElement(); + } + + XmlWriter::ScopedElement& XmlWriter::ScopedElement::writeText( std::string const& text, bool indent ) { + m_writer->writeText( text, indent ); + return *this; + } + + XmlWriter::XmlWriter( std::ostream& os ) : m_os( os ) + { + writeDeclaration(); + } + + XmlWriter::~XmlWriter() { + while( !m_tags.empty() ) + endElement(); + } + + XmlWriter& XmlWriter::startElement( std::string const& name ) { + ensureTagClosed(); + newlineIfNecessary(); + m_os << m_indent << '<' << name; + m_tags.push_back( name ); + m_indent += " "; + m_tagIsOpen = true; + return *this; + } + + XmlWriter::ScopedElement XmlWriter::scopedElement( std::string const& name ) { + ScopedElement scoped( this ); + startElement( name ); + return scoped; + } + + XmlWriter& XmlWriter::endElement() { + newlineIfNecessary(); + m_indent = m_indent.substr( 0, m_indent.size()-2 ); + if( m_tagIsOpen ) { + m_os << "/>"; + m_tagIsOpen = false; + } + else { + m_os << m_indent << ""; + } + m_os << std::endl; + m_tags.pop_back(); + return *this; + } + + XmlWriter& XmlWriter::writeAttribute( std::string const& name, std::string const& attribute ) { + if( !name.empty() && !attribute.empty() ) + m_os << ' ' << name << "=\"" << XmlEncode( attribute, XmlEncode::ForAttributes ) << '"'; + return *this; + } + + XmlWriter& XmlWriter::writeAttribute( std::string const& name, bool attribute ) { + m_os << ' ' << name << "=\"" << ( attribute ? "true" : "false" ) << '"'; + return *this; + } + + XmlWriter& XmlWriter::writeText( std::string const& text, bool indent ) { + if( !text.empty() ){ + bool tagWasOpen = m_tagIsOpen; + ensureTagClosed(); + if( tagWasOpen && indent ) + m_os << m_indent; + m_os << XmlEncode( text ); + m_needsNewline = true; + } + return *this; + } + + XmlWriter& XmlWriter::writeComment( std::string const& text ) { + ensureTagClosed(); + m_os << m_indent << ""; + m_needsNewline = true; + return *this; + } + + void XmlWriter::writeStylesheetRef( std::string const& url ) { + m_os << "\n"; + } + + XmlWriter& XmlWriter::writeBlankLine() { + ensureTagClosed(); + m_os << '\n'; + return *this; + } + + void XmlWriter::ensureTagClosed() { + if( m_tagIsOpen ) { + m_os << ">" << std::endl; + m_tagIsOpen = false; + } + } + + void XmlWriter::writeDeclaration() { + m_os << "\n"; + } + + void XmlWriter::newlineIfNecessary() { + if( m_needsNewline ) { + m_os << std::endl; + m_needsNewline = false; + } + } +} +// end catch_xmlwriter.cpp +// start catch_reporter_bases.cpp + +#include +#include +#include +#include +#include + +namespace Catch { + void prepareExpandedExpression(AssertionResult& result) { + result.getExpandedExpression(); + } + + // Because formatting using c++ streams is stateful, drop down to C is required + // Alternatively we could use stringstream, but its performance is... not good. + std::string getFormattedDuration( double duration ) { + // Max exponent + 1 is required to represent the whole part + // + 1 for decimal point + // + 3 for the 3 decimal places + // + 1 for null terminator + const size_t maxDoubleSize = DBL_MAX_10_EXP + 1 + 1 + 3 + 1; + char buffer[maxDoubleSize]; + + // Save previous errno, to prevent sprintf from overwriting it + ErrnoGuard guard; +#ifdef _MSC_VER + sprintf_s(buffer, "%.3f", duration); +#else + sprintf(buffer, "%.3f", duration); +#endif + return std::string(buffer); + } + + TestEventListenerBase::TestEventListenerBase(ReporterConfig const & _config) + :StreamingReporterBase(_config) {} + + void TestEventListenerBase::assertionStarting(AssertionInfo const &) {} + + bool TestEventListenerBase::assertionEnded(AssertionStats const &) { + return false; + } + +} // end namespace Catch +// end catch_reporter_bases.cpp +// start catch_reporter_compact.cpp + +namespace { + +#ifdef CATCH_PLATFORM_MAC + const char* failedString() { return "FAILED"; } + const char* passedString() { return "PASSED"; } +#else + const char* failedString() { return "failed"; } + const char* passedString() { return "passed"; } +#endif + + // Colour::LightGrey + Catch::Colour::Code dimColour() { return Catch::Colour::FileName; } + + std::string bothOrAll( std::size_t count ) { + return count == 1 ? std::string() : + count == 2 ? "both " : "all " ; + } +} + +namespace Catch { + + struct CompactReporter : StreamingReporterBase { + + using StreamingReporterBase::StreamingReporterBase; + + ~CompactReporter() override; + + static std::string getDescription() { + return "Reports test results on a single line, suitable for IDEs"; + } + + ReporterPreferences getPreferences() const override { + ReporterPreferences prefs; + prefs.shouldRedirectStdOut = false; + return prefs; + } + + void noMatchingTestCases( std::string const& spec ) override { + stream << "No test cases matched '" << spec << '\'' << std::endl; + } + + void assertionStarting( AssertionInfo const& ) override {} + + bool assertionEnded( AssertionStats const& _assertionStats ) override { + AssertionResult const& result = _assertionStats.assertionResult; + + bool printInfoMessages = true; + + // Drop out if result was successful and we're not printing those + if( !m_config->includeSuccessfulResults() && result.isOk() ) { + if( result.getResultType() != ResultWas::Warning ) + return false; + printInfoMessages = false; + } + + AssertionPrinter printer( stream, _assertionStats, printInfoMessages ); + printer.print(); + + stream << std::endl; + return true; + } + + void sectionEnded(SectionStats const& _sectionStats) override { + if (m_config->showDurations() == ShowDurations::Always) { + stream << getFormattedDuration(_sectionStats.durationInSeconds) << " s: " << _sectionStats.sectionInfo.name << std::endl; + } + } + + void testRunEnded( TestRunStats const& _testRunStats ) override { + printTotals( _testRunStats.totals ); + stream << '\n' << std::endl; + StreamingReporterBase::testRunEnded( _testRunStats ); + } + + private: + class AssertionPrinter { + public: + AssertionPrinter& operator= ( AssertionPrinter const& ) = delete; + AssertionPrinter( AssertionPrinter const& ) = delete; + AssertionPrinter( std::ostream& _stream, AssertionStats const& _stats, bool _printInfoMessages ) + : stream( _stream ) + , result( _stats.assertionResult ) + , messages( _stats.infoMessages ) + , itMessage( _stats.infoMessages.begin() ) + , printInfoMessages( _printInfoMessages ) + {} + + void print() { + printSourceInfo(); + + itMessage = messages.begin(); + + switch( result.getResultType() ) { + case ResultWas::Ok: + printResultType( Colour::ResultSuccess, passedString() ); + printOriginalExpression(); + printReconstructedExpression(); + if ( ! result.hasExpression() ) + printRemainingMessages( Colour::None ); + else + printRemainingMessages(); + break; + case ResultWas::ExpressionFailed: + if( result.isOk() ) + printResultType( Colour::ResultSuccess, failedString() + std::string( " - but was ok" ) ); + else + printResultType( Colour::Error, failedString() ); + printOriginalExpression(); + printReconstructedExpression(); + printRemainingMessages(); + break; + case ResultWas::ThrewException: + printResultType( Colour::Error, failedString() ); + printIssue( "unexpected exception with message:" ); + printMessage(); + printExpressionWas(); + printRemainingMessages(); + break; + case ResultWas::FatalErrorCondition: + printResultType( Colour::Error, failedString() ); + printIssue( "fatal error condition with message:" ); + printMessage(); + printExpressionWas(); + printRemainingMessages(); + break; + case ResultWas::DidntThrowException: + printResultType( Colour::Error, failedString() ); + printIssue( "expected exception, got none" ); + printExpressionWas(); + printRemainingMessages(); + break; + case ResultWas::Info: + printResultType( Colour::None, "info" ); + printMessage(); + printRemainingMessages(); + break; + case ResultWas::Warning: + printResultType( Colour::None, "warning" ); + printMessage(); + printRemainingMessages(); + break; + case ResultWas::ExplicitFailure: + printResultType( Colour::Error, failedString() ); + printIssue( "explicitly" ); + printRemainingMessages( Colour::None ); + break; + // These cases are here to prevent compiler warnings + case ResultWas::Unknown: + case ResultWas::FailureBit: + case ResultWas::Exception: + printResultType( Colour::Error, "** internal error **" ); + break; + } + } + + private: + void printSourceInfo() const { + Colour colourGuard( Colour::FileName ); + stream << result.getSourceInfo() << ':'; + } + + void printResultType( Colour::Code colour, std::string const& passOrFail ) const { + if( !passOrFail.empty() ) { + { + Colour colourGuard( colour ); + stream << ' ' << passOrFail; + } + stream << ':'; + } + } + + void printIssue( std::string const& issue ) const { + stream << ' ' << issue; + } + + void printExpressionWas() { + if( result.hasExpression() ) { + stream << ';'; + { + Colour colour( dimColour() ); + stream << " expression was:"; + } + printOriginalExpression(); + } + } + + void printOriginalExpression() const { + if( result.hasExpression() ) { + stream << ' ' << result.getExpression(); + } + } + + void printReconstructedExpression() const { + if( result.hasExpandedExpression() ) { + { + Colour colour( dimColour() ); + stream << " for: "; + } + stream << result.getExpandedExpression(); + } + } + + void printMessage() { + if ( itMessage != messages.end() ) { + stream << " '" << itMessage->message << '\''; + ++itMessage; + } + } + + void printRemainingMessages( Colour::Code colour = dimColour() ) { + if ( itMessage == messages.end() ) + return; + + // using messages.end() directly yields (or auto) compilation error: + std::vector::const_iterator itEnd = messages.end(); + const std::size_t N = static_cast( std::distance( itMessage, itEnd ) ); + + { + Colour colourGuard( colour ); + stream << " with " << pluralise( N, "message" ) << ':'; + } + + for(; itMessage != itEnd; ) { + // If this assertion is a warning ignore any INFO messages + if( printInfoMessages || itMessage->type != ResultWas::Info ) { + stream << " '" << itMessage->message << '\''; + if ( ++itMessage != itEnd ) { + Colour colourGuard( dimColour() ); + stream << " and"; + } + } + } + } + + private: + std::ostream& stream; + AssertionResult const& result; + std::vector messages; + std::vector::const_iterator itMessage; + bool printInfoMessages; + }; + + // Colour, message variants: + // - white: No tests ran. + // - red: Failed [both/all] N test cases, failed [both/all] M assertions. + // - white: Passed [both/all] N test cases (no assertions). + // - red: Failed N tests cases, failed M assertions. + // - green: Passed [both/all] N tests cases with M assertions. + + void printTotals( const Totals& totals ) const { + if( totals.testCases.total() == 0 ) { + stream << "No tests ran."; + } + else if( totals.testCases.failed == totals.testCases.total() ) { + Colour colour( Colour::ResultError ); + const std::string qualify_assertions_failed = + totals.assertions.failed == totals.assertions.total() ? + bothOrAll( totals.assertions.failed ) : std::string(); + stream << + "Failed " << bothOrAll( totals.testCases.failed ) + << pluralise( totals.testCases.failed, "test case" ) << ", " + "failed " << qualify_assertions_failed << + pluralise( totals.assertions.failed, "assertion" ) << '.'; + } + else if( totals.assertions.total() == 0 ) { + stream << + "Passed " << bothOrAll( totals.testCases.total() ) + << pluralise( totals.testCases.total(), "test case" ) + << " (no assertions)."; + } + else if( totals.assertions.failed ) { + Colour colour( Colour::ResultError ); + stream << + "Failed " << pluralise( totals.testCases.failed, "test case" ) << ", " + "failed " << pluralise( totals.assertions.failed, "assertion" ) << '.'; + } + else { + Colour colour( Colour::ResultSuccess ); + stream << + "Passed " << bothOrAll( totals.testCases.passed ) + << pluralise( totals.testCases.passed, "test case" ) << + " with " << pluralise( totals.assertions.passed, "assertion" ) << '.'; + } + } + }; + + CompactReporter::~CompactReporter() {} + + CATCH_REGISTER_REPORTER( "compact", CompactReporter ) + +} // end namespace Catch +// end catch_reporter_compact.cpp +// start catch_reporter_console.cpp + +#include +#include + +namespace { + std::size_t makeRatio( std::size_t number, std::size_t total ) { + std::size_t ratio = total > 0 ? CATCH_CONFIG_CONSOLE_WIDTH * number/ total : 0; + return ( ratio == 0 && number > 0 ) ? 1 : ratio; + } + + std::size_t& findMax( std::size_t& i, std::size_t& j, std::size_t& k ) { + if( i > j && i > k ) + return i; + else if( j > k ) + return j; + else + return k; + } + + struct ColumnInfo { + enum Justification { Left, Right }; + std::string name; + int width; + Justification justification; + }; + struct ColumnBreak {}; + struct RowBreak {}; + + class TablePrinter { + std::ostream& m_os; + std::vector m_columnInfos; + std::ostringstream m_oss; + int m_currentColumn = -1; + bool m_isOpen = false; + + public: + TablePrinter( std::ostream& os, std::vector const& columnInfos ) + : m_os( os ), + m_columnInfos( columnInfos ) + {} + + auto columnInfos() const -> std::vector const& { + return m_columnInfos; + } + + void open() { + if( !m_isOpen ) { + m_isOpen = true; + *this << RowBreak(); + for( auto const& info : m_columnInfos ) + *this << info.name << ColumnBreak(); + *this << RowBreak(); + m_os << Catch::getLineOfChars<'-'>() << "\n"; + } + } + void close() { + if( m_isOpen ) { + *this << RowBreak(); + m_os << std::endl; + m_isOpen = false; + } + } + + template + friend TablePrinter& operator << ( TablePrinter& tp, T const& value ) { + tp.m_oss << value; + return tp; + } + + friend TablePrinter& operator << ( TablePrinter& tp, ColumnBreak ) { + auto colStr = tp.m_oss.str(); + // This takes account of utf8 encodings + auto strSize = Catch::StringRef( colStr ).numberOfCharacters(); + tp.m_oss.str(""); + tp.open(); + if( tp.m_currentColumn == static_cast(tp.m_columnInfos.size()-1) ) { + tp.m_currentColumn = -1; + tp.m_os << "\n"; + } + tp.m_currentColumn++; + + auto colInfo = tp.m_columnInfos[tp.m_currentColumn]; + auto padding = ( strSize+2 < static_cast( colInfo.width ) ) + ? std::string( colInfo.width-(strSize+2), ' ' ) + : std::string(); + if( colInfo.justification == ColumnInfo::Left ) + tp.m_os << colStr << padding << " "; + else + tp.m_os << padding << colStr << " "; + return tp; + } + + friend TablePrinter& operator << ( TablePrinter& tp, RowBreak ) { + if( tp.m_currentColumn > 0 ) { + tp.m_os << "\n"; + tp.m_currentColumn = -1; + } + return tp; + } + }; + + class Duration { + enum class Unit { + Auto, + Nanoseconds, + Microseconds, + Milliseconds, + Seconds, + Minutes + }; + static const uint64_t s_nanosecondsInAMicrosecond = 1000; + static const uint64_t s_nanosecondsInAMillisecond = 1000*s_nanosecondsInAMicrosecond; + static const uint64_t s_nanosecondsInASecond = 1000*s_nanosecondsInAMillisecond; + static const uint64_t s_nanosecondsInAMinute = 60*s_nanosecondsInASecond; + + uint64_t m_inNanoseconds; + Unit m_units; + + public: + Duration( uint64_t inNanoseconds, Unit units = Unit::Auto ) + : m_inNanoseconds( inNanoseconds ), + m_units( units ) + { + if( m_units == Unit::Auto ) { + if( m_inNanoseconds < s_nanosecondsInAMicrosecond ) + m_units = Unit::Nanoseconds; + else if( m_inNanoseconds < s_nanosecondsInAMillisecond ) + m_units = Unit::Microseconds; + else if( m_inNanoseconds < s_nanosecondsInASecond ) + m_units = Unit::Milliseconds; + else if( m_inNanoseconds < s_nanosecondsInAMinute ) + m_units = Unit::Seconds; + else + m_units = Unit::Minutes; + } + + } + + auto value() const -> double { + switch( m_units ) { + case Unit::Microseconds: + return m_inNanoseconds / static_cast( s_nanosecondsInAMicrosecond ); + case Unit::Milliseconds: + return m_inNanoseconds / static_cast( s_nanosecondsInAMillisecond ); + case Unit::Seconds: + return m_inNanoseconds / static_cast( s_nanosecondsInASecond ); + case Unit::Minutes: + return m_inNanoseconds / static_cast( s_nanosecondsInAMinute ); + default: + return static_cast( m_inNanoseconds ); + } + } + auto unitsAsString() const -> std::string { + switch( m_units ) { + case Unit::Nanoseconds: + return "ns"; + case Unit::Microseconds: + return "µs"; + case Unit::Milliseconds: + return "ms"; + case Unit::Seconds: + return "s"; + case Unit::Minutes: + return "m"; + default: + return "** internal error **"; + } + + } + friend auto operator << ( std::ostream& os, Duration const& duration ) -> std::ostream& { + return os << duration.value() << " " << duration.unitsAsString(); + } + }; +} + +namespace Catch { + + struct ConsoleReporter : StreamingReporterBase { + TablePrinter m_tablePrinter; + + ConsoleReporter( ReporterConfig const& config ) + : StreamingReporterBase( config ), + m_tablePrinter( config.stream(), + { + { "benchmark name", CATCH_CONFIG_CONSOLE_WIDTH-32, ColumnInfo::Left }, + { "iters", 8, ColumnInfo::Right }, + { "elapsed ns", 14, ColumnInfo::Right }, + { "average", 14, ColumnInfo::Right } + } ) + {} + ~ConsoleReporter() override; + static std::string getDescription() { + return "Reports test results as plain lines of text"; + } + + void noMatchingTestCases( std::string const& spec ) override { + stream << "No test cases matched '" << spec << '\'' << std::endl; + } + + void assertionStarting( AssertionInfo const& ) override { + } + + bool assertionEnded( AssertionStats const& _assertionStats ) override { + AssertionResult const& result = _assertionStats.assertionResult; + + bool includeResults = m_config->includeSuccessfulResults() || !result.isOk(); + + // Drop out if result was successful but we're not printing them. + if( !includeResults && result.getResultType() != ResultWas::Warning ) + return false; + + lazyPrint(); + + AssertionPrinter printer( stream, _assertionStats, includeResults ); + printer.print(); + stream << std::endl; + return true; + } + + void sectionStarting( SectionInfo const& _sectionInfo ) override { + m_headerPrinted = false; + StreamingReporterBase::sectionStarting( _sectionInfo ); + } + void sectionEnded( SectionStats const& _sectionStats ) override { + m_tablePrinter.close(); + if( _sectionStats.missingAssertions ) { + lazyPrint(); + Colour colour( Colour::ResultError ); + if( m_sectionStack.size() > 1 ) + stream << "\nNo assertions in section"; + else + stream << "\nNo assertions in test case"; + stream << " '" << _sectionStats.sectionInfo.name << "'\n" << std::endl; + } + if( m_config->showDurations() == ShowDurations::Always ) { + stream << getFormattedDuration(_sectionStats.durationInSeconds) << " s: " << _sectionStats.sectionInfo.name << std::endl; + } + if( m_headerPrinted ) { + m_headerPrinted = false; + } + StreamingReporterBase::sectionEnded( _sectionStats ); + } + + void benchmarkStarting( BenchmarkInfo const& info ) override { + lazyPrintWithoutClosingBenchmarkTable(); + + auto nameCol = Column( info.name ).width( m_tablePrinter.columnInfos()[0].width-2 ); + + bool firstLine = true; + for( auto line : nameCol ) { + if( !firstLine ) + m_tablePrinter << ColumnBreak() << ColumnBreak() << ColumnBreak(); + else + firstLine = false; + + m_tablePrinter << line << ColumnBreak(); + } + } + void benchmarkEnded( BenchmarkStats const& stats ) override { + Duration average( stats.elapsedTimeInNanoseconds/stats.iterations ); + m_tablePrinter + << stats.iterations << ColumnBreak() + << stats.elapsedTimeInNanoseconds << ColumnBreak() + << average << ColumnBreak(); + } + + void testCaseEnded( TestCaseStats const& _testCaseStats ) override { + m_tablePrinter.close(); + StreamingReporterBase::testCaseEnded( _testCaseStats ); + m_headerPrinted = false; + } + void testGroupEnded( TestGroupStats const& _testGroupStats ) override { + if( currentGroupInfo.used ) { + printSummaryDivider(); + stream << "Summary for group '" << _testGroupStats.groupInfo.name << "':\n"; + printTotals( _testGroupStats.totals ); + stream << '\n' << std::endl; + } + StreamingReporterBase::testGroupEnded( _testGroupStats ); + } + void testRunEnded( TestRunStats const& _testRunStats ) override { + printTotalsDivider( _testRunStats.totals ); + printTotals( _testRunStats.totals ); + stream << std::endl; + StreamingReporterBase::testRunEnded( _testRunStats ); + } + + private: + + class AssertionPrinter { + public: + AssertionPrinter& operator= ( AssertionPrinter const& ) = delete; + AssertionPrinter( AssertionPrinter const& ) = delete; + AssertionPrinter( std::ostream& _stream, AssertionStats const& _stats, bool _printInfoMessages ) + : stream( _stream ), + stats( _stats ), + result( _stats.assertionResult ), + colour( Colour::None ), + message( result.getMessage() ), + messages( _stats.infoMessages ), + printInfoMessages( _printInfoMessages ) + { + switch( result.getResultType() ) { + case ResultWas::Ok: + colour = Colour::Success; + passOrFail = "PASSED"; + //if( result.hasMessage() ) + if( _stats.infoMessages.size() == 1 ) + messageLabel = "with message"; + if( _stats.infoMessages.size() > 1 ) + messageLabel = "with messages"; + break; + case ResultWas::ExpressionFailed: + if( result.isOk() ) { + colour = Colour::Success; + passOrFail = "FAILED - but was ok"; + } + else { + colour = Colour::Error; + passOrFail = "FAILED"; + } + if( _stats.infoMessages.size() == 1 ) + messageLabel = "with message"; + if( _stats.infoMessages.size() > 1 ) + messageLabel = "with messages"; + break; + case ResultWas::ThrewException: + colour = Colour::Error; + passOrFail = "FAILED"; + messageLabel = "due to unexpected exception with "; + if (_stats.infoMessages.size() == 1) + messageLabel += "message"; + if (_stats.infoMessages.size() > 1) + messageLabel += "messages"; + break; + case ResultWas::FatalErrorCondition: + colour = Colour::Error; + passOrFail = "FAILED"; + messageLabel = "due to a fatal error condition"; + break; + case ResultWas::DidntThrowException: + colour = Colour::Error; + passOrFail = "FAILED"; + messageLabel = "because no exception was thrown where one was expected"; + break; + case ResultWas::Info: + messageLabel = "info"; + break; + case ResultWas::Warning: + messageLabel = "warning"; + break; + case ResultWas::ExplicitFailure: + passOrFail = "FAILED"; + colour = Colour::Error; + if( _stats.infoMessages.size() == 1 ) + messageLabel = "explicitly with message"; + if( _stats.infoMessages.size() > 1 ) + messageLabel = "explicitly with messages"; + break; + // These cases are here to prevent compiler warnings + case ResultWas::Unknown: + case ResultWas::FailureBit: + case ResultWas::Exception: + passOrFail = "** internal error **"; + colour = Colour::Error; + break; + } + } + + void print() const { + printSourceInfo(); + if( stats.totals.assertions.total() > 0 ) { + if( result.isOk() ) + stream << '\n'; + printResultType(); + printOriginalExpression(); + printReconstructedExpression(); + } + else { + stream << '\n'; + } + printMessage(); + } + + private: + void printResultType() const { + if( !passOrFail.empty() ) { + Colour colourGuard( colour ); + stream << passOrFail << ":\n"; + } + } + void printOriginalExpression() const { + if( result.hasExpression() ) { + Colour colourGuard( Colour::OriginalExpression ); + stream << " "; + stream << result.getExpressionInMacro(); + stream << '\n'; + } + } + void printReconstructedExpression() const { + if( result.hasExpandedExpression() ) { + stream << "with expansion:\n"; + Colour colourGuard( Colour::ReconstructedExpression ); + stream << Column( result.getExpandedExpression() ).indent(2) << '\n'; + } + } + void printMessage() const { + if( !messageLabel.empty() ) + stream << messageLabel << ':' << '\n'; + for( auto const& msg : messages ) { + // If this assertion is a warning ignore any INFO messages + if( printInfoMessages || msg.type != ResultWas::Info ) + stream << Column( msg.message ).indent(2) << '\n'; + } + } + void printSourceInfo() const { + Colour colourGuard( Colour::FileName ); + stream << result.getSourceInfo() << ": "; + } + + std::ostream& stream; + AssertionStats const& stats; + AssertionResult const& result; + Colour::Code colour; + std::string passOrFail; + std::string messageLabel; + std::string message; + std::vector messages; + bool printInfoMessages; + }; + + void lazyPrint() { + + m_tablePrinter.close(); + lazyPrintWithoutClosingBenchmarkTable(); + } + + void lazyPrintWithoutClosingBenchmarkTable() { + + if( !currentTestRunInfo.used ) + lazyPrintRunInfo(); + if( !currentGroupInfo.used ) + lazyPrintGroupInfo(); + + if( !m_headerPrinted ) { + printTestCaseAndSectionHeader(); + m_headerPrinted = true; + } + } + void lazyPrintRunInfo() { + stream << '\n' << getLineOfChars<'~'>() << '\n'; + Colour colour( Colour::SecondaryText ); + stream << currentTestRunInfo->name + << " is a Catch v" << libraryVersion() << " host application.\n" + << "Run with -? for options\n\n"; + + if( m_config->rngSeed() != 0 ) + stream << "Randomness seeded to: " << m_config->rngSeed() << "\n\n"; + + currentTestRunInfo.used = true; + } + void lazyPrintGroupInfo() { + if( !currentGroupInfo->name.empty() && currentGroupInfo->groupsCounts > 1 ) { + printClosedHeader( "Group: " + currentGroupInfo->name ); + currentGroupInfo.used = true; + } + } + void printTestCaseAndSectionHeader() { + assert( !m_sectionStack.empty() ); + printOpenHeader( currentTestCaseInfo->name ); + + if( m_sectionStack.size() > 1 ) { + Colour colourGuard( Colour::Headers ); + + auto + it = m_sectionStack.begin()+1, // Skip first section (test case) + itEnd = m_sectionStack.end(); + for( ; it != itEnd; ++it ) + printHeaderString( it->name, 2 ); + } + + SourceLineInfo lineInfo = m_sectionStack.back().lineInfo; + + if( !lineInfo.empty() ){ + stream << getLineOfChars<'-'>() << '\n'; + Colour colourGuard( Colour::FileName ); + stream << lineInfo << '\n'; + } + stream << getLineOfChars<'.'>() << '\n' << std::endl; + } + + void printClosedHeader( std::string const& _name ) { + printOpenHeader( _name ); + stream << getLineOfChars<'.'>() << '\n'; + } + void printOpenHeader( std::string const& _name ) { + stream << getLineOfChars<'-'>() << '\n'; + { + Colour colourGuard( Colour::Headers ); + printHeaderString( _name ); + } + } + + // if string has a : in first line will set indent to follow it on + // subsequent lines + void printHeaderString( std::string const& _string, std::size_t indent = 0 ) { + std::size_t i = _string.find( ": " ); + if( i != std::string::npos ) + i+=2; + else + i = 0; + stream << Column( _string ).indent( indent+i ).initialIndent( indent ) << '\n'; + } + + struct SummaryColumn { + + SummaryColumn( std::string const& _label, Colour::Code _colour ) + : label( _label ), + colour( _colour ) + {} + SummaryColumn addRow( std::size_t count ) { + std::ostringstream oss; + oss << count; + std::string row = oss.str(); + for( auto& oldRow : rows ) { + while( oldRow.size() < row.size() ) + oldRow = ' ' + oldRow; + while( oldRow.size() > row.size() ) + row = ' ' + row; + } + rows.push_back( row ); + return *this; + } + + std::string label; + Colour::Code colour; + std::vector rows; + + }; + + void printTotals( Totals const& totals ) { + if( totals.testCases.total() == 0 ) { + stream << Colour( Colour::Warning ) << "No tests ran\n"; + } + else if( totals.assertions.total() > 0 && totals.testCases.allPassed() ) { + stream << Colour( Colour::ResultSuccess ) << "All tests passed"; + stream << " (" + << pluralise( totals.assertions.passed, "assertion" ) << " in " + << pluralise( totals.testCases.passed, "test case" ) << ')' + << '\n'; + } + else { + + std::vector columns; + columns.push_back( SummaryColumn( "", Colour::None ) + .addRow( totals.testCases.total() ) + .addRow( totals.assertions.total() ) ); + columns.push_back( SummaryColumn( "passed", Colour::Success ) + .addRow( totals.testCases.passed ) + .addRow( totals.assertions.passed ) ); + columns.push_back( SummaryColumn( "failed", Colour::ResultError ) + .addRow( totals.testCases.failed ) + .addRow( totals.assertions.failed ) ); + columns.push_back( SummaryColumn( "failed as expected", Colour::ResultExpectedFailure ) + .addRow( totals.testCases.failedButOk ) + .addRow( totals.assertions.failedButOk ) ); + + printSummaryRow( "test cases", columns, 0 ); + printSummaryRow( "assertions", columns, 1 ); + } + } + void printSummaryRow( std::string const& label, std::vector const& cols, std::size_t row ) { + for( auto col : cols ) { + std::string value = col.rows[row]; + if( col.label.empty() ) { + stream << label << ": "; + if( value != "0" ) + stream << value; + else + stream << Colour( Colour::Warning ) << "- none -"; + } + else if( value != "0" ) { + stream << Colour( Colour::LightGrey ) << " | "; + stream << Colour( col.colour ) + << value << ' ' << col.label; + } + } + stream << '\n'; + } + + void printTotalsDivider( Totals const& totals ) { + if( totals.testCases.total() > 0 ) { + std::size_t failedRatio = makeRatio( totals.testCases.failed, totals.testCases.total() ); + std::size_t failedButOkRatio = makeRatio( totals.testCases.failedButOk, totals.testCases.total() ); + std::size_t passedRatio = makeRatio( totals.testCases.passed, totals.testCases.total() ); + while( failedRatio + failedButOkRatio + passedRatio < CATCH_CONFIG_CONSOLE_WIDTH-1 ) + findMax( failedRatio, failedButOkRatio, passedRatio )++; + while( failedRatio + failedButOkRatio + passedRatio > CATCH_CONFIG_CONSOLE_WIDTH-1 ) + findMax( failedRatio, failedButOkRatio, passedRatio )--; + + stream << Colour( Colour::Error ) << std::string( failedRatio, '=' ); + stream << Colour( Colour::ResultExpectedFailure ) << std::string( failedButOkRatio, '=' ); + if( totals.testCases.allPassed() ) + stream << Colour( Colour::ResultSuccess ) << std::string( passedRatio, '=' ); + else + stream << Colour( Colour::Success ) << std::string( passedRatio, '=' ); + } + else { + stream << Colour( Colour::Warning ) << std::string( CATCH_CONFIG_CONSOLE_WIDTH-1, '=' ); + } + stream << '\n'; + } + void printSummaryDivider() { + stream << getLineOfChars<'-'>() << '\n'; + } + + private: + bool m_headerPrinted = false; + }; + + CATCH_REGISTER_REPORTER( "console", ConsoleReporter ) + + ConsoleReporter::~ConsoleReporter() {} + +} // end namespace Catch +// end catch_reporter_console.cpp +// start catch_reporter_junit.cpp + +#include + +#include +#include + +namespace Catch { + + namespace { + std::string getCurrentTimestamp() { + // Beware, this is not reentrant because of backward compatibility issues + // Also, UTC only, again because of backward compatibility (%z is C++11) + time_t rawtime; + std::time(&rawtime); + const size_t timeStampSize = sizeof("2017-01-16T17:06:45Z"); + +#ifdef _MSC_VER + std::tm timeInfo = {}; + gmtime_s(&timeInfo, &rawtime); +#else + std::tm* timeInfo; + timeInfo = std::gmtime(&rawtime); +#endif + + char timeStamp[timeStampSize]; + const char * const fmt = "%Y-%m-%dT%H:%M:%SZ"; + +#ifdef _MSC_VER + std::strftime(timeStamp, timeStampSize, fmt, &timeInfo); +#else + std::strftime(timeStamp, timeStampSize, fmt, timeInfo); +#endif + return std::string(timeStamp); + } + + std::string fileNameTag(const std::vector &tags) { + auto it = std::find_if(begin(tags), + end(tags), + [] (std::string const& tag) {return tag.front() == '#'; }); + if (it != tags.end()) + return it->substr(1); + return std::string(); + } + } + + class JunitReporter : public CumulativeReporterBase { + public: + JunitReporter( ReporterConfig const& _config ) + : CumulativeReporterBase( _config ), + xml( _config.stream() ) + { + m_reporterPrefs.shouldRedirectStdOut = true; + } + + ~JunitReporter() override; + + static std::string getDescription() { + return "Reports test results in an XML format that looks like Ant's junitreport target"; + } + + void noMatchingTestCases( std::string const& /*spec*/ ) override {} + + void testRunStarting( TestRunInfo const& runInfo ) override { + CumulativeReporterBase::testRunStarting( runInfo ); + xml.startElement( "testsuites" ); + } + + void testGroupStarting( GroupInfo const& groupInfo ) override { + suiteTimer.start(); + stdOutForSuite.str(""); + stdErrForSuite.str(""); + unexpectedExceptions = 0; + CumulativeReporterBase::testGroupStarting( groupInfo ); + } + + void testCaseStarting( TestCaseInfo const& testCaseInfo ) override { + m_okToFail = testCaseInfo.okToFail(); + } + bool assertionEnded( AssertionStats const& assertionStats ) override { + if( assertionStats.assertionResult.getResultType() == ResultWas::ThrewException && !m_okToFail ) + unexpectedExceptions++; + return CumulativeReporterBase::assertionEnded( assertionStats ); + } + + void testCaseEnded( TestCaseStats const& testCaseStats ) override { + stdOutForSuite << testCaseStats.stdOut; + stdErrForSuite << testCaseStats.stdErr; + CumulativeReporterBase::testCaseEnded( testCaseStats ); + } + + void testGroupEnded( TestGroupStats const& testGroupStats ) override { + double suiteTime = suiteTimer.getElapsedSeconds(); + CumulativeReporterBase::testGroupEnded( testGroupStats ); + writeGroup( *m_testGroups.back(), suiteTime ); + } + + void testRunEndedCumulative() override { + xml.endElement(); + } + + void writeGroup( TestGroupNode const& groupNode, double suiteTime ) { + XmlWriter::ScopedElement e = xml.scopedElement( "testsuite" ); + TestGroupStats const& stats = groupNode.value; + xml.writeAttribute( "name", stats.groupInfo.name ); + xml.writeAttribute( "errors", unexpectedExceptions ); + xml.writeAttribute( "failures", stats.totals.assertions.failed-unexpectedExceptions ); + xml.writeAttribute( "tests", stats.totals.assertions.total() ); + xml.writeAttribute( "hostname", "tbd" ); // !TBD + if( m_config->showDurations() == ShowDurations::Never ) + xml.writeAttribute( "time", "" ); + else + xml.writeAttribute( "time", suiteTime ); + xml.writeAttribute( "timestamp", getCurrentTimestamp() ); + + // Write test cases + for( auto const& child : groupNode.children ) + writeTestCase( *child ); + + xml.scopedElement( "system-out" ).writeText( trim( stdOutForSuite.str() ), false ); + xml.scopedElement( "system-err" ).writeText( trim( stdErrForSuite.str() ), false ); + } + + void writeTestCase( TestCaseNode const& testCaseNode ) { + TestCaseStats const& stats = testCaseNode.value; + + // All test cases have exactly one section - which represents the + // test case itself. That section may have 0-n nested sections + assert( testCaseNode.children.size() == 1 ); + SectionNode const& rootSection = *testCaseNode.children.front(); + + std::string className = stats.testInfo.className; + + if( className.empty() ) { + className = fileNameTag(stats.testInfo.tags); + if ( className.empty() ) + className = "global"; + } + + if ( !m_config->name().empty() ) + className = m_config->name() + "." + className; + + writeSection( className, "", rootSection ); + } + + void writeSection( std::string const& className, + std::string const& rootName, + SectionNode const& sectionNode ) { + std::string name = trim( sectionNode.stats.sectionInfo.name ); + if( !rootName.empty() ) + name = rootName + '/' + name; + + if( !sectionNode.assertions.empty() || + !sectionNode.stdOut.empty() || + !sectionNode.stdErr.empty() ) { + XmlWriter::ScopedElement e = xml.scopedElement( "testcase" ); + if( className.empty() ) { + xml.writeAttribute( "classname", name ); + xml.writeAttribute( "name", "root" ); + } + else { + xml.writeAttribute( "classname", className ); + xml.writeAttribute( "name", name ); + } + xml.writeAttribute( "time", ::Catch::Detail::stringify( sectionNode.stats.durationInSeconds ) ); + + writeAssertions( sectionNode ); + + if( !sectionNode.stdOut.empty() ) + xml.scopedElement( "system-out" ).writeText( trim( sectionNode.stdOut ), false ); + if( !sectionNode.stdErr.empty() ) + xml.scopedElement( "system-err" ).writeText( trim( sectionNode.stdErr ), false ); + } + for( auto const& childNode : sectionNode.childSections ) + if( className.empty() ) + writeSection( name, "", *childNode ); + else + writeSection( className, name, *childNode ); + } + + void writeAssertions( SectionNode const& sectionNode ) { + for( auto const& assertion : sectionNode.assertions ) + writeAssertion( assertion ); + } + void writeAssertion( AssertionStats const& stats ) { + AssertionResult const& result = stats.assertionResult; + if( !result.isOk() ) { + std::string elementName; + switch( result.getResultType() ) { + case ResultWas::ThrewException: + case ResultWas::FatalErrorCondition: + elementName = "error"; + break; + case ResultWas::ExplicitFailure: + elementName = "failure"; + break; + case ResultWas::ExpressionFailed: + elementName = "failure"; + break; + case ResultWas::DidntThrowException: + elementName = "failure"; + break; + + // We should never see these here: + case ResultWas::Info: + case ResultWas::Warning: + case ResultWas::Ok: + case ResultWas::Unknown: + case ResultWas::FailureBit: + case ResultWas::Exception: + elementName = "internalError"; + break; + } + + XmlWriter::ScopedElement e = xml.scopedElement( elementName ); + + xml.writeAttribute( "message", result.getExpandedExpression() ); + xml.writeAttribute( "type", result.getTestMacroName() ); + + std::ostringstream oss; + if( !result.getMessage().empty() ) + oss << result.getMessage() << '\n'; + for( auto const& msg : stats.infoMessages ) + if( msg.type == ResultWas::Info ) + oss << msg.message << '\n'; + + oss << "at " << result.getSourceInfo(); + xml.writeText( oss.str(), false ); + } + } + + XmlWriter xml; + Timer suiteTimer; + std::ostringstream stdOutForSuite; + std::ostringstream stdErrForSuite; + unsigned int unexpectedExceptions = 0; + bool m_okToFail = false; + }; + + JunitReporter::~JunitReporter() {} + CATCH_REGISTER_REPORTER( "junit", JunitReporter ) + +} // end namespace Catch +// end catch_reporter_junit.cpp +// start catch_reporter_multi.cpp + +namespace Catch { + + void MultipleReporters::add( IStreamingReporterPtr&& reporter ) { + m_reporters.push_back( std::move( reporter ) ); + } + + ReporterPreferences MultipleReporters::getPreferences() const { + return m_reporters[0]->getPreferences(); + } + + std::set MultipleReporters::getSupportedVerbosities() { + return { }; + } + + void MultipleReporters::noMatchingTestCases( std::string const& spec ) { + for( auto const& reporter : m_reporters ) + reporter->noMatchingTestCases( spec ); + } + + void MultipleReporters::testRunStarting( TestRunInfo const& testRunInfo ) { + for( auto const& reporter : m_reporters ) + reporter->testRunStarting( testRunInfo ); + } + + void MultipleReporters::testGroupStarting( GroupInfo const& groupInfo ) { + for( auto const& reporter : m_reporters ) + reporter->testGroupStarting( groupInfo ); + } + + void MultipleReporters::testCaseStarting( TestCaseInfo const& testInfo ) { + for( auto const& reporter : m_reporters ) + reporter->testCaseStarting( testInfo ); + } + + void MultipleReporters::sectionStarting( SectionInfo const& sectionInfo ) { + for( auto const& reporter : m_reporters ) + reporter->sectionStarting( sectionInfo ); + } + + void MultipleReporters::assertionStarting( AssertionInfo const& assertionInfo ) { + for( auto const& reporter : m_reporters ) + reporter->assertionStarting( assertionInfo ); + } + + // The return value indicates if the messages buffer should be cleared: + bool MultipleReporters::assertionEnded( AssertionStats const& assertionStats ) { + bool clearBuffer = false; + for( auto const& reporter : m_reporters ) + clearBuffer |= reporter->assertionEnded( assertionStats ); + return clearBuffer; + } + + void MultipleReporters::sectionEnded( SectionStats const& sectionStats ) { + for( auto const& reporter : m_reporters ) + reporter->sectionEnded( sectionStats ); + } + + void MultipleReporters::testCaseEnded( TestCaseStats const& testCaseStats ) { + for( auto const& reporter : m_reporters ) + reporter->testCaseEnded( testCaseStats ); + } + + void MultipleReporters::testGroupEnded( TestGroupStats const& testGroupStats ) { + for( auto const& reporter : m_reporters ) + reporter->testGroupEnded( testGroupStats ); + } + + void MultipleReporters::testRunEnded( TestRunStats const& testRunStats ) { + for( auto const& reporter : m_reporters ) + reporter->testRunEnded( testRunStats ); + } + + void MultipleReporters::skipTest( TestCaseInfo const& testInfo ) { + for( auto const& reporter : m_reporters ) + reporter->skipTest( testInfo ); + } + + bool MultipleReporters::isMulti() const { + return true; + } + +} // end namespace Catch +// end catch_reporter_multi.cpp +// start catch_reporter_xml.cpp + +namespace Catch { + class XmlReporter : public StreamingReporterBase { + public: + XmlReporter( ReporterConfig const& _config ) + : StreamingReporterBase( _config ), + m_xml(_config.stream()) + { + m_reporterPrefs.shouldRedirectStdOut = true; + } + + ~XmlReporter() override; + + static std::string getDescription() { + return "Reports test results as an XML document"; + } + + virtual std::string getStylesheetRef() const { + return std::string(); + } + + void writeSourceInfo( SourceLineInfo const& sourceInfo ) { + m_xml + .writeAttribute( "filename", sourceInfo.file ) + .writeAttribute( "line", sourceInfo.line ); + } + + public: // StreamingReporterBase + + void noMatchingTestCases( std::string const& s ) override { + StreamingReporterBase::noMatchingTestCases( s ); + } + + void testRunStarting( TestRunInfo const& testInfo ) override { + StreamingReporterBase::testRunStarting( testInfo ); + std::string stylesheetRef = getStylesheetRef(); + if( !stylesheetRef.empty() ) + m_xml.writeStylesheetRef( stylesheetRef ); + m_xml.startElement( "Catch" ); + if( !m_config->name().empty() ) + m_xml.writeAttribute( "name", m_config->name() ); + } + + void testGroupStarting( GroupInfo const& groupInfo ) override { + StreamingReporterBase::testGroupStarting( groupInfo ); + m_xml.startElement( "Group" ) + .writeAttribute( "name", groupInfo.name ); + } + + void testCaseStarting( TestCaseInfo const& testInfo ) override { + StreamingReporterBase::testCaseStarting(testInfo); + m_xml.startElement( "TestCase" ) + .writeAttribute( "name", trim( testInfo.name ) ) + .writeAttribute( "description", testInfo.description ) + .writeAttribute( "tags", testInfo.tagsAsString() ); + + writeSourceInfo( testInfo.lineInfo ); + + if ( m_config->showDurations() == ShowDurations::Always ) + m_testCaseTimer.start(); + m_xml.ensureTagClosed(); + } + + void sectionStarting( SectionInfo const& sectionInfo ) override { + StreamingReporterBase::sectionStarting( sectionInfo ); + if( m_sectionDepth++ > 0 ) { + m_xml.startElement( "Section" ) + .writeAttribute( "name", trim( sectionInfo.name ) ) + .writeAttribute( "description", sectionInfo.description ); + writeSourceInfo( sectionInfo.lineInfo ); + m_xml.ensureTagClosed(); + } + } + + void assertionStarting( AssertionInfo const& ) override { } + + bool assertionEnded( AssertionStats const& assertionStats ) override { + + AssertionResult const& result = assertionStats.assertionResult; + + bool includeResults = m_config->includeSuccessfulResults() || !result.isOk(); + + if( includeResults ) { + // Print any info messages in tags. + for( auto const& msg : assertionStats.infoMessages ) { + if( msg.type == ResultWas::Info ) { + m_xml.scopedElement( "Info" ) + .writeText( msg.message ); + } else if ( msg.type == ResultWas::Warning ) { + m_xml.scopedElement( "Warning" ) + .writeText( msg.message ); + } + } + } + + // Drop out if result was successful but we're not printing them. + if( !includeResults && result.getResultType() != ResultWas::Warning ) + return true; + + // Print the expression if there is one. + if( result.hasExpression() ) { + m_xml.startElement( "Expression" ) + .writeAttribute( "success", result.succeeded() ) + .writeAttribute( "type", result.getTestMacroName() ); + + writeSourceInfo( result.getSourceInfo() ); + + m_xml.scopedElement( "Original" ) + .writeText( result.getExpression() ); + m_xml.scopedElement( "Expanded" ) + .writeText( result.getExpandedExpression() ); + } + + // And... Print a result applicable to each result type. + switch( result.getResultType() ) { + case ResultWas::ThrewException: + m_xml.startElement( "Exception" ); + writeSourceInfo( result.getSourceInfo() ); + m_xml.writeText( result.getMessage() ); + m_xml.endElement(); + break; + case ResultWas::FatalErrorCondition: + m_xml.startElement( "FatalErrorCondition" ); + writeSourceInfo( result.getSourceInfo() ); + m_xml.writeText( result.getMessage() ); + m_xml.endElement(); + break; + case ResultWas::Info: + m_xml.scopedElement( "Info" ) + .writeText( result.getMessage() ); + break; + case ResultWas::Warning: + // Warning will already have been written + break; + case ResultWas::ExplicitFailure: + m_xml.startElement( "Failure" ); + writeSourceInfo( result.getSourceInfo() ); + m_xml.writeText( result.getMessage() ); + m_xml.endElement(); + break; + default: + break; + } + + if( result.hasExpression() ) + m_xml.endElement(); + + return true; + } + + void sectionEnded( SectionStats const& sectionStats ) override { + StreamingReporterBase::sectionEnded( sectionStats ); + if( --m_sectionDepth > 0 ) { + XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResults" ); + e.writeAttribute( "successes", sectionStats.assertions.passed ); + e.writeAttribute( "failures", sectionStats.assertions.failed ); + e.writeAttribute( "expectedFailures", sectionStats.assertions.failedButOk ); + + if ( m_config->showDurations() == ShowDurations::Always ) + e.writeAttribute( "durationInSeconds", sectionStats.durationInSeconds ); + + m_xml.endElement(); + } + } + + void testCaseEnded( TestCaseStats const& testCaseStats ) override { + StreamingReporterBase::testCaseEnded( testCaseStats ); + XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResult" ); + e.writeAttribute( "success", testCaseStats.totals.assertions.allOk() ); + + if ( m_config->showDurations() == ShowDurations::Always ) + e.writeAttribute( "durationInSeconds", m_testCaseTimer.getElapsedSeconds() ); + + if( !testCaseStats.stdOut.empty() ) + m_xml.scopedElement( "StdOut" ).writeText( trim( testCaseStats.stdOut ), false ); + if( !testCaseStats.stdErr.empty() ) + m_xml.scopedElement( "StdErr" ).writeText( trim( testCaseStats.stdErr ), false ); + + m_xml.endElement(); + } + + void testGroupEnded( TestGroupStats const& testGroupStats ) override { + StreamingReporterBase::testGroupEnded( testGroupStats ); + // TODO: Check testGroupStats.aborting and act accordingly. + m_xml.scopedElement( "OverallResults" ) + .writeAttribute( "successes", testGroupStats.totals.assertions.passed ) + .writeAttribute( "failures", testGroupStats.totals.assertions.failed ) + .writeAttribute( "expectedFailures", testGroupStats.totals.assertions.failedButOk ); + m_xml.endElement(); + } + + void testRunEnded( TestRunStats const& testRunStats ) override { + StreamingReporterBase::testRunEnded( testRunStats ); + m_xml.scopedElement( "OverallResults" ) + .writeAttribute( "successes", testRunStats.totals.assertions.passed ) + .writeAttribute( "failures", testRunStats.totals.assertions.failed ) + .writeAttribute( "expectedFailures", testRunStats.totals.assertions.failedButOk ); + m_xml.endElement(); + } + + private: + Timer m_testCaseTimer; + XmlWriter m_xml; + int m_sectionDepth = 0; + }; + + XmlReporter::~XmlReporter() {} + CATCH_REGISTER_REPORTER( "xml", XmlReporter ) + +} // end namespace Catch +// end catch_reporter_xml.cpp + +namespace Catch { + LeakDetector leakDetector; + + // These are all here to avoid warnings about not having any out of line + // virtual methods + NonCopyable::~NonCopyable() {} + IStream::~IStream() noexcept {} + FileStream::~FileStream() noexcept {} + CoutStream::~CoutStream() noexcept {} + DebugOutStream::~DebugOutStream() noexcept {} + StreamBufBase::~StreamBufBase() noexcept {} + IContext::~IContext() {} + IResultCapture::~IResultCapture() {} + ITestInvoker::~ITestInvoker() {} + ITestCaseRegistry::~ITestCaseRegistry() {} + IRegistryHub::~IRegistryHub() {} + IMutableRegistryHub::~IMutableRegistryHub() {} + IExceptionTranslator::~IExceptionTranslator() {} + IExceptionTranslatorRegistry::~IExceptionTranslatorRegistry() {} + IRunner::~IRunner() {} + IMutableContext::~IMutableContext() {} + IConfig::~IConfig() {} + + void Config::dummy() {} +} + +#ifdef __clang__ +#pragma clang diagnostic pop +#endif + +// end catch_impl.hpp +#endif + +#ifdef CATCH_CONFIG_MAIN +// start catch_default_main.hpp + +#ifndef __OBJC__ + +#if defined(WIN32) && defined(_UNICODE) && !defined(DO_NOT_USE_WMAIN) +// Standard C/C++ Win32 Unicode wmain entry point +extern "C" int wmain (int argc, wchar_t * argv[], wchar_t * []) { +#else +// Standard C/C++ main entry point +int main (int argc, char * argv[]) { +#endif + + return Catch::Session().run( argc, argv ); +} + +#else // __OBJC__ + +// Objective-C entry point +int main (int argc, char * const argv[]) { +#if !CATCH_ARC_ENABLED + NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init]; +#endif + + Catch::registerTestMethods(); + int result = Catch::Session().run( argc, (char* const*)argv ); + +#if !CATCH_ARC_ENABLED + [pool drain]; +#endif + + return result; +} + +#endif // __OBJC__ + +// end catch_default_main.hpp +#endif + +#ifdef CLARA_CONFIG_MAIN_NOT_DEFINED +# undef CLARA_CONFIG_MAIN +#endif + +////// +// If this config identifier is defined then all CATCH macros are prefixed with CATCH_ +#ifdef CATCH_CONFIG_PREFIX_ALL + +#define CATCH_REQUIRE( ... ) INTERNAL_CATCH_TEST( "CATCH_REQUIRE", Catch::ResultDisposition::Normal, __VA_ARGS__ ) +#define CATCH_REQUIRE_FALSE( ... ) INTERNAL_CATCH_TEST( "CATCH_REQUIRE_FALSE", Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) + +#define CATCH_REQUIRE_THROWS( ... ) INTERNAL_CATCH_THROWS( "CATCH_REQUIRE_THROWS", Catch::ResultDisposition::Normal, "", __VA_ARGS__ ) +#define CATCH_REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CATCH_REQUIRE_THROWS_AS", exceptionType, Catch::ResultDisposition::Normal, expr ) +#define CATCH_REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CATCH_REQUIRE_THROWS_WITH", Catch::ResultDisposition::Normal, matcher, expr ) +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define CATCH_REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CATCH_REQUIRE_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::Normal, matcher, expr ) +#endif// CATCH_CONFIG_DISABLE_MATCHERS +#define CATCH_REQUIRE_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CATCH_REQUIRE_NOTHROW", Catch::ResultDisposition::Normal, __VA_ARGS__ ) + +#define CATCH_CHECK( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CATCH_CHECK_FALSE( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK_FALSE", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) +#define CATCH_CHECKED_IF( ... ) INTERNAL_CATCH_IF( "CATCH_CHECKED_IF", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CATCH_CHECKED_ELSE( ... ) INTERNAL_CATCH_ELSE( "CATCH_CHECKED_ELSE", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CATCH_CHECK_NOFAIL( ... ) INTERNAL_CATCH_TEST( "CATCH_CHECK_NOFAIL", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, __VA_ARGS__ ) + +#define CATCH_CHECK_THROWS( ... ) INTERNAL_CATCH_THROWS( "CATCH_CHECK_THROWS", Catch::ResultDisposition::ContinueOnFailure, "", __VA_ARGS__ ) +#define CATCH_CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CATCH_CHECK_THROWS_AS", exceptionType, Catch::ResultDisposition::ContinueOnFailure, expr ) +#define CATCH_CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CATCH_CHECK_THROWS_WITH", Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define CATCH_CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CATCH_CHECK_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) +#endif // CATCH_CONFIG_DISABLE_MATCHERS +#define CATCH_CHECK_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CATCH_CHECK_NOTHROW", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) + +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define CATCH_CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CATCH_CHECK_THAT", matcher, Catch::ResultDisposition::ContinueOnFailure, arg ) + +#define CATCH_REQUIRE_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CATCH_REQUIRE_THAT", matcher, Catch::ResultDisposition::Normal, arg ) +#endif // CATCH_CONFIG_DISABLE_MATCHERS + +#define CATCH_INFO( msg ) INTERNAL_CATCH_INFO( "CATCH_INFO", msg ) +#define CATCH_WARN( msg ) INTERNAL_CATCH_MSG( "CATCH_WARN", Catch::ResultWas::Warning, Catch::ResultDisposition::ContinueOnFailure, msg ) +#define CATCH_CAPTURE( msg ) INTERNAL_CATCH_INFO( "CATCH_CAPTURE", #msg " := " << ::Catch::Detail::stringify(msg) ) + +#define CATCH_TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ ) +#define CATCH_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ ) +#define CATCH_METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ ) +#define CATCH_REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ ) +#define CATCH_SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ ) +#define CATCH_FAIL( ... ) INTERNAL_CATCH_MSG( "CATCH_FAIL", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, __VA_ARGS__ ) +#define CATCH_FAIL_CHECK( ... ) INTERNAL_CATCH_MSG( "CATCH_FAIL_CHECK", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CATCH_SUCCEED( ... ) INTERNAL_CATCH_MSG( "CATCH_SUCCEED", Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) + +#define CATCH_ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE() + +// "BDD-style" convenience wrappers +#define CATCH_SCENARIO( ... ) CATCH_TEST_CASE( "Scenario: " __VA_ARGS__ ) +#define CATCH_SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " __VA_ARGS__ ) +#define CATCH_GIVEN( desc ) CATCH_SECTION( std::string( "Given: ") + desc ) +#define CATCH_WHEN( desc ) CATCH_SECTION( std::string( " When: ") + desc ) +#define CATCH_AND_WHEN( desc ) CATCH_SECTION( std::string( " And: ") + desc ) +#define CATCH_THEN( desc ) CATCH_SECTION( std::string( " Then: ") + desc ) +#define CATCH_AND_THEN( desc ) CATCH_SECTION( std::string( " And: ") + desc ) + +// If CATCH_CONFIG_PREFIX_ALL is not defined then the CATCH_ prefix is not required +#else + +#define REQUIRE( ... ) INTERNAL_CATCH_TEST( "REQUIRE", Catch::ResultDisposition::Normal, __VA_ARGS__ ) +#define REQUIRE_FALSE( ... ) INTERNAL_CATCH_TEST( "REQUIRE_FALSE", Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) + +#define REQUIRE_THROWS( ... ) INTERNAL_CATCH_THROWS( "REQUIRE_THROWS", Catch::ResultDisposition::Normal, __VA_ARGS__ ) +#define REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "REQUIRE_THROWS_AS", exceptionType, Catch::ResultDisposition::Normal, expr ) +#define REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "REQUIRE_THROWS_WITH", Catch::ResultDisposition::Normal, matcher, expr ) +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define REQUIRE_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "REQUIRE_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::Normal, matcher, expr ) +#endif // CATCH_CONFIG_DISABLE_MATCHERS +#define REQUIRE_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "REQUIRE_NOTHROW", Catch::ResultDisposition::Normal, __VA_ARGS__ ) + +#define CHECK( ... ) INTERNAL_CATCH_TEST( "CHECK", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CHECK_FALSE( ... ) INTERNAL_CATCH_TEST( "CHECK_FALSE", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::FalseTest, __VA_ARGS__ ) +#define CHECKED_IF( ... ) INTERNAL_CATCH_IF( "CHECKED_IF", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CHECKED_ELSE( ... ) INTERNAL_CATCH_ELSE( "CHECKED_ELSE", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CHECK_NOFAIL( ... ) INTERNAL_CATCH_TEST( "CHECK_NOFAIL", Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, __VA_ARGS__ ) + +#define CHECK_THROWS( ... ) INTERNAL_CATCH_THROWS( "CHECK_THROWS", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( "CHECK_THROWS_AS", exceptionType, Catch::ResultDisposition::ContinueOnFailure, expr ) +#define CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS_STR_MATCHES( "CHECK_THROWS_WITH", Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define CHECK_THROWS_MATCHES( expr, exceptionType, matcher ) INTERNAL_CATCH_THROWS_MATCHES( "CHECK_THROWS_MATCHES", exceptionType, Catch::ResultDisposition::ContinueOnFailure, matcher, expr ) +#endif // CATCH_CONFIG_DISABLE_MATCHERS +#define CHECK_NOTHROW( ... ) INTERNAL_CATCH_NO_THROW( "CHECK_NOTHROW", Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) + +#if !defined(CATCH_CONFIG_DISABLE_MATCHERS) +#define CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "CHECK_THAT", matcher, Catch::ResultDisposition::ContinueOnFailure, arg ) + +#define REQUIRE_THAT( arg, matcher ) INTERNAL_CHECK_THAT( "REQUIRE_THAT", matcher, Catch::ResultDisposition::Normal, arg ) +#endif // CATCH_CONFIG_DISABLE_MATCHERS + +#define INFO( msg ) INTERNAL_CATCH_INFO( "INFO", msg ) +#define WARN( msg ) INTERNAL_CATCH_MSG( "WARN", Catch::ResultWas::Warning, Catch::ResultDisposition::ContinueOnFailure, msg ) +#define CAPTURE( msg ) INTERNAL_CATCH_INFO( "CAPTURE", #msg " := " << ::Catch::Detail::stringify(msg) ) + +#define TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ ) +#define TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ ) +#define METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ ) +#define REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ ) +#define SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ ) +#define FAIL( ... ) INTERNAL_CATCH_MSG( "FAIL", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, __VA_ARGS__ ) +#define FAIL_CHECK( ... ) INTERNAL_CATCH_MSG( "FAIL_CHECK", Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define SUCCEED( ... ) INTERNAL_CATCH_MSG( "SUCCEED", Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, __VA_ARGS__ ) +#define ANON_TEST_CASE() INTERNAL_CATCH_TESTCASE() + +#endif + +#define CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) + +// "BDD-style" convenience wrappers +#define SCENARIO( ... ) TEST_CASE( "Scenario: " __VA_ARGS__ ) +#define SCENARIO_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " __VA_ARGS__ ) + +#define GIVEN( desc ) SECTION( std::string(" Given: ") + desc ) +#define WHEN( desc ) SECTION( std::string(" When: ") + desc ) +#define AND_WHEN( desc ) SECTION( std::string("And when: ") + desc ) +#define THEN( desc ) SECTION( std::string(" Then: ") + desc ) +#define AND_THEN( desc ) SECTION( std::string(" And: ") + desc ) + +using Catch::Detail::Approx; + +// start catch_reenable_warnings.h + + +#ifdef __clang__ +# ifdef __ICC // icpc defines the __clang__ macro +# pragma warning(pop) +# else +# pragma clang diagnostic pop +# endif +#elif defined __GNUC__ +# pragma GCC diagnostic pop +#endif + +// end catch_reenable_warnings.h +// end catch.hpp +#endif // TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED + diff -Nru adapterremoval-2.2.2/tests/unit/fastq_enc_test.cpp adapterremoval-2.2.3/tests/unit/fastq_enc_test.cpp --- adapterremoval-2.2.2/tests/unit/fastq_enc_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/fastq_enc_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,43 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#include "testing.hpp" +#include "fastq.hpp" + + +namespace ar +{ + +/////////////////////////////////////////////////////////////////////////////// +// Names (default objects) + +TEST_CASE("Global encodings have expected names", "[fastq_encoding]") +{ + REQUIRE(FASTQ_ENCODING_33.name() == std::string("Phred+33")); + REQUIRE(FASTQ_ENCODING_64.name() == std::string("Phred+64")); + REQUIRE(FASTQ_ENCODING_SAM.name() == std::string("Phred+33")); + REQUIRE(FASTQ_ENCODING_SOLEXA.name() == std::string("Solexa")); +} + +} diff -Nru adapterremoval-2.2.2/tests/unit/fastq_test.cpp adapterremoval-2.2.3/tests/unit/fastq_test.cpp --- adapterremoval-2.2.2/tests/unit/fastq_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/fastq_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,1155 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#include +#include + +#include "testing.hpp" +#include "debug.hpp" +#include "fastq.hpp" +#include "linereader.hpp" + +namespace ar +{ + +class vec_reader : public line_reader_base +{ +public: + vec_reader(const string_vec& lines) + : m_lines(lines) + , m_it(m_lines.begin()) + { + } + + bool getline(std::string& dst) { + if (m_it == m_lines.end()) { + return false; + } + + dst = *m_it++; + return true; + } + +private: + string_vec m_lines; + string_vec::const_iterator m_it; +}; + + + +/////////////////////////////////////////////////////////////////////////////// +// Default constructor + +TEST_CASE("default_constructor", "[fastq::fastq]") +{ + const fastq record; + REQUIRE(record.header() == ""); + REQUIRE(record.sequence() == ""); + REQUIRE(record.qualities() == ""); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Primary constructor + +TEST_CASE("constructor_empty_fields", "[fastq::fastq]") +{ + const fastq record("", "", ""); + REQUIRE(record.header() == ""); + REQUIRE(record.sequence() == ""); + REQUIRE(record.qualities() == ""); +} + + +TEST_CASE("constructor_simple_record_phred_33_encoded", "[fastq::fastq]") +{ + const fastq record("record_1", "ACGAGTCA", "!7BF8DGI"); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); +} + + +TEST_CASE("constructor_simple_record_phred_64_encoded", "[fastq::fastq]") +{ + const fastq record("record_2", "ACGAGTCA", "@VaeWcfh", FASTQ_ENCODING_64); + REQUIRE(record.header() == "record_2"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); +} + + +TEST_CASE("constructor_simple_record_phred_solexa_encoded", "[fastq::fastq]") +{ + const fastq record("record_3", "AAACGAGTCA", ";h>S\\TCDUJ", FASTQ_ENCODING_SOLEXA); + REQUIRE(record.header() == "record_3"); + REQUIRE(record.sequence() == "AAACGAGTCA"); + REQUIRE(record.qualities() == "\"I#4=5&&6+"); +} + + +TEST_CASE("constructor_simple_record_lowercase_to_uppercase", "[fastq::fastq]") +{ + const fastq record("record_1", "AnGaGtcA", "!7BF8DGI"); + REQUIRE(record.sequence() == "ANGAGTCA"); +} + + +TEST_CASE("constructor_simple_record_dots_to_n", "[fastq::fastq]") +{ + const fastq record("record_1", "AC.AG.C.", "!7BF8DGI"); + REQUIRE(record.sequence() == "ACNAGNCN"); +} + + +TEST_CASE("constructor_score_boundries_phred_33", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_33)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_33), fastq_error); + + REQUIRE_NOTHROW(fastq("Rec", "CAT", "IJJ", FASTQ_ENCODING_33)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", "IJK", FASTQ_ENCODING_33), fastq_error); +} + + +TEST_CASE("constructor_score_boundries_phred_64", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Rec", "CAT", "@@A", FASTQ_ENCODING_64)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", "?@A", FASTQ_ENCODING_64), fastq_error); + + REQUIRE_NOTHROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_64)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_64), fastq_error); +} + + +TEST_CASE("constructor_score_boundries_solexa", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Rec", "CAT", ";;<", FASTQ_ENCODING_SOLEXA)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", ":;<", FASTQ_ENCODING_SOLEXA), fastq_error); + + REQUIRE_NOTHROW(fastq("Rec", "CAT", "ghi", FASTQ_ENCODING_SOLEXA)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", "ghj", FASTQ_ENCODING_SOLEXA), fastq_error); +} + +TEST_CASE("constructor_score_boundries_ignored", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Rec", "CAT", "!!\"", FASTQ_ENCODING_SAM)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", " !\"", FASTQ_ENCODING_SAM), fastq_error); + + REQUIRE_NOTHROW(fastq("Rec", "CAT", "gh~", FASTQ_ENCODING_SAM)); + REQUIRE_THROWS_AS(fastq("Rec", "CAT", "gh\x7f", FASTQ_ENCODING_SAM), fastq_error); +} + + +TEST_CASE("constructor_field_lengths", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Name", "CAT", "IJJ")); + // A non-empty sequence must be specified + REQUIRE_THROWS_AS(fastq("Name", "", "IJJ"), fastq_error); + // A non-empty quality string must be specified + REQUIRE_THROWS_AS(fastq("Name", "CAT", ""), fastq_error); + // And the length of each must be the same + REQUIRE_THROWS_AS(fastq("Name", "CA", "IJJ"), fastq_error); + REQUIRE_THROWS_AS(fastq("Name", "CAT", "IJ"), fastq_error); +} + + +TEST_CASE("constructor_invalid_nucleotides", "[fastq::fastq]") +{ + REQUIRE_NOTHROW(fastq("Name", "CATT", "IJJI")); + // Non-alpha characters are not allowed + REQUIRE_THROWS_AS(fastq("Name", "CAT!", "IJJI"), fastq_error); + // Numeric charecters are not allowed + REQUIRE_THROWS_AS(fastq("Name", "CAT7", "IJJI"), fastq_error); + // But neither are non acgtn/ACGTN allowed + REQUIRE_THROWS_AS(fastq("Name", "CATS", "IJJI"), fastq_error); + REQUIRE_THROWS_AS(fastq("Name", "CATs", "IJJI"), fastq_error); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Constructor without qualities + +TEST_CASE("constructor_no_qualities", "[fastq::fastq]") +{ + const fastq record("record_1", "ACGT"); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == "ACGT"); + REQUIRE(record.qualities() == "!!!!"); +} + + +TEST_CASE("constructor_no_qualities_no_sequence", "[fastq::fastq]") +{ + const fastq record("record_1", ""); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == ""); + REQUIRE(record.qualities() == ""); +} + + +/////////////////////////////////////////////////////////////////////////////// +// misc properties + +TEST_CASE("name", "[fastq::fastq]") +{ + REQUIRE(fastq("name", "", "").name() == "name"); + REQUIRE(fastq("name meta", "", "").name() == "name"); + REQUIRE(fastq("name meta more", "", "").name() == "name"); +} + + +TEST_CASE("length", "[fastq::fastq]") +{ + REQUIRE(fastq("record_1", "", "").length() == 0); + REQUIRE(fastq("record_1", "A", "G").length() == 1); + REQUIRE(fastq("record_1", "AC", "!B").length() == 2); + REQUIRE(fastq("record_1", "ACG", "!7B").length() == 3); +} + + +TEST_CASE("count_ns", "[fastq::fastq]") +{ + REQUIRE(fastq("Rec", "ACGTA", "IJIJI").count_ns() == 0); + REQUIRE(fastq("Rec", "ANGTA", "IJIJI").count_ns() == 1); + REQUIRE(fastq("Rec", "ANGTN", "IJIJI").count_ns() == 2); + REQUIRE(fastq("Rec", "ANGNN", "IJIJI").count_ns() == 3); + REQUIRE(fastq("Rec", "NNGNN", "IJIJI").count_ns() == 4); + REQUIRE(fastq("Rec", "NNNNN", "IJIJI").count_ns() == 5); +} + + +/////////////////////////////////////////////////////////////////////////////// +// trim_trailing_bases + +TEST_CASE("trim_trailing_bases__empty_record", "[fastq::fastq]") +{ + fastq record("Empty", "", ""); + const fastq::ntrimmed expected(0, 0); + REQUIRE(record.trim_trailing_bases(true, 10) == expected); + REQUIRE(record == fastq("Empty", "", "")); +} + + +TEST_CASE("trim_trailing_bases__trim_nothing", "[fastq::fastq]") +{ + const fastq reference("Rec", "NNNNN", "!!!!!"); + const fastq::ntrimmed expected(0, 0); + fastq record = reference; + + // Trim neither Ns nor low Phred score bases + REQUIRE(record.trim_trailing_bases(false, -1) == expected); + REQUIRE(record == reference); +} + + +TEST_CASE("trim_trailing_bases__trim_ns", "[fastq::fastq]") +{ + fastq record("Rec", "NNANT", "23456"); + const fastq expected_record("Rec", "ANT", "456"); + const fastq::ntrimmed expected_ntrim(2, 0); + + REQUIRE(record.trim_trailing_bases(true, -1) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +TEST_CASE("trim_trailing_bases__trim_trailing_bases", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "TN", "%$"); + const fastq::ntrimmed expected_ntrim(0, 3); + fastq record("Rec", "TNANT", "%$#!\""); + + REQUIRE(record.trim_trailing_bases(false, 2) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +TEST_CASE("trim_trailing_bases__trim_mixed", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "TAG", "$12"); + const fastq::ntrimmed expected_ntrim(3, 2); + fastq record("Rec", "NTNTAGNT", "1!#$12#\""); + + REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +TEST_CASE("trim_trailing_bases__trim_mixed__no_low_quality_bases", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "ACTTAG", "12I$12"); + const fastq::ntrimmed expected_ntrim(0, 0); + fastq record = expected_record; + + REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +TEST_CASE("trim_trailing_bases__trim_everything", "[fastq::fastq]") +{ + fastq record("Rec", "TAG", "!!!"); + const fastq expected_record = fastq("Rec", "", ""); + const fastq::ntrimmed expected_ntrim(0, 3); + REQUIRE(record.trim_trailing_bases(true, 2) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +/////////////////////////////////////////////////////////////////////////////// +// trim_windowed_bases + +TEST_CASE("Window trimming with invalid parameters", "[fastq::windows]") +{ + const std::vector values = {-1.0, std::numeric_limits::quiet_NaN()}; + for (const auto& value : values) { + fastq record("Rec", "TAGTGACAT", "111111111"); + REQUIRE_THROWS_AS(record.trim_windowed_bases(false, -1, value), assert_failed); + } +} + + +TEST_CASE("Window trimming empty reads", "[fastq::windows]") +{ + const std::vector values = {1, 0.1, 3}; + for (const auto& value : values) { + fastq record("Empty", "", ""); + const fastq::ntrimmed expected(0, 0); + REQUIRE(record.trim_windowed_bases(true, 10, value) == expected); + REQUIRE(record == fastq("Empty", "", "")); + } +} + + +TEST_CASE("Window trimming entire read", "[fastq::windows]") +{ + const std::vector values = {1, 0.2, 4, 10}; + for (const auto& value : values) { + fastq record("Rec", "TAGTGACAT", "111111111"); + const fastq expected_record = fastq("Rec", "", ""); + const fastq::ntrimmed expected_ntrim(9, 0); + REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming nothing", "[fastq::windows]") +{ + const std::vector values = {0, 1, 0.2, 3, 4, 5, 6, 7, 8, 9, 10, 11}; + for (const auto& value : values) { + fastq record("Rec", "TAGTGACAT", "111111111"); + const fastq expected_record = record; + const fastq::ntrimmed expected_ntrim(0, 0); + REQUIRE(record.trim_windowed_bases(false, -1, value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming of Ns", "[fastq::windows]") +{ + const std::vector values = {1, 0.2}; + for (const auto& value : values) { + fastq record("Rec", "NNATNT", "234567"); + const fastq expected_record("Rec", "ATNT", "4567"); + const fastq::ntrimmed expected_ntrim(2, 0); + + REQUIRE(record.trim_windowed_bases(true, -1, value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming of Ns, final window contains Ns", "[fastq::windows]") +{ + const std::vector values = {2, 3, 4}; + for (const auto& value : values) { + fastq record("Rec", "NNATNT", "234567"); + const fastq expected_record("Rec", "AT", "45"); + const fastq::ntrimmed expected_ntrim(2, 2); + + REQUIRE(record.trim_windowed_bases(true, -1, value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming of Ns, no valid window found", "[fastq::fastq]") +{ + fastq record("Rec", "NNATNT", "234567"); + const fastq expected_record("Rec", "", ""); + const fastq::ntrimmed expected_ntrim(6, 0); + + REQUIRE(record.trim_windowed_bases(true, -1, 5) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +TEST_CASE("Window trimming 5p only, 1bp", "[fastq::windows]") +{ + const std::vector values = {1, 0.1}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATCCG", "0123456789"); + const fastq expected_record("Rec", "CGATCCG", "3456789"); + const fastq::ntrimmed expected_ntrim(3, 0); + + REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming 5p only, 2bp", "[fastq::windows]") +{ + const std::vector values = {2, 0.2}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATCCG", "0123456789"); + const fastq expected_record("Rec", "CGATCCG", "3456789"); + const fastq::ntrimmed expected_ntrim(3, 0); + + REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming 5p only, inclusive lower bound", "[fastq::windows]") +{ + const std::vector values = {2, 3}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATCCG", "0123126789"); + const fastq expected_record("Rec", "TCCG", "6789"); + const fastq::ntrimmed expected_ntrim(6, 0); + + REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming 3p only, inclusive lower bound", "[fastq::windows]") +{ + const std::vector values = {3}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATCCG", "9876312333"); + const fastq expected_record("Rec", "TAACG", "98763"); + const fastq::ntrimmed expected_ntrim(0, 5); + + REQUIRE(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming big and small windows #1", "[fastq::windows]") +{ + const std::vector values = {0, 0.01, 20}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATC", "23456789"); + const fastq expected_record("Rec", "", ""); + const fastq::ntrimmed expected_ntrim(8, 0); + + CHECK(record.trim_windowed_bases(false, '2' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming big and small windows #2", "[fastq::windows]") +{ + const std::vector values = {0, 0.01, 20}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATC", "23456780"); + const fastq expected_record("Rec", "TAACGAT", "2345678"); + const fastq::ntrimmed expected_ntrim(0, 1); + + REQUIRE(record.trim_windowed_bases(false, '1' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("Window trimming last trailing window", "[fastq::windows]") +{ + const std::vector values = {1, 2, 3, 4, 5, 6, 7, 8, 9}; + for (const auto& value : values) { + fastq record("Rec", "TAACGATCC", "234567811"); + const fastq expected_record("Rec", "TAACGAT", "2345678"); + const fastq::ntrimmed expected_ntrim(0, 2); + + REQUIRE(record.trim_windowed_bases(false, '1' - '!', value) == expected_ntrim); + REQUIRE(record == expected_record); + } +} + + +TEST_CASE("trim_windowed_bases__trim_window", "[fastq::fastq]") +{ + // Should trim starting at the window of low quality bases in the middle + // even with high qual bases at the end. + fastq record("Rec", "NNAAAAAAAAATNNNNNNNA", "##EEEEEEEEEE#######E"); + const fastq expected_record = fastq("Rec", "AAAAAAAAAT", "EEEEEEEEEE"); + const fastq::ntrimmed expected_ntrim(2, 8); + REQUIRE(record.trim_windowed_bases(true, 10, 5) == expected_ntrim); + REQUIRE(record == expected_record); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Truncate + +TEST_CASE("truncate_empty", "[fastq::fastq]") +{ + fastq record("Empty", "", ""); + record.truncate(0, 10); + REQUIRE(record == fastq("Empty", "", "")); +} + + +TEST_CASE("truncate_zero_bases", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "ACTTAG", "12I$12"); + fastq current_record = expected_record; + current_record.truncate(); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_all_bases", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "", ""); + fastq current_record("Rec", "ACTTAG", "12I$12"); + current_record.truncate(1, 0); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_5p", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "TTAG", "I$12"); + fastq current_record("Rec", "ACTTAG", "12I$12"); + current_record.truncate(2); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_3p", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "ACT", "12I"); + fastq current_record("Rec", "ACTTAG", "12I$12"); + current_record.truncate(0, 3); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_middle", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "TTA", "I$1"); + fastq current_record("Rec", "ACTTAG", "12I$12"); + current_record.truncate(2, 3); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_len_higher_than_n_bases", "[fastq::fastq]") +{ + const fastq expected_record("Rec", "TTAG", "I$12"); + fastq current_record("Rec", "ACTTAG", "12I$12"); + current_record.truncate(2, 1024); + REQUIRE(current_record == expected_record); +} + + +TEST_CASE("truncate_pos_after_last_base", "[fastq::fastq]") +{ + // Same behavior as string::substr + fastq current_record("Rec", "ACTTAG", "12I$12"); + REQUIRE_NOTHROW(current_record.truncate(6)); + REQUIRE_THROWS_AS(current_record.truncate(7), std::out_of_range); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Reverse complement + +TEST_CASE("reverse_complement__empty", "[fastq::fastq]") +{ + const fastq expected = fastq("Empty", "", ""); + fastq result = fastq("Empty", "", ""); + result.reverse_complement(); + REQUIRE(result == expected); +} + + +TEST_CASE("reverse_complement", "[fastq::fastq]") +{ + const fastq expected = fastq("Rec", "TACAGANGTN", "0123456789"); + fastq result = fastq("Rec", "NACNTCTGTA", "9876543210"); + result.reverse_complement(); + REQUIRE(result == expected); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Adding prefixes to the header + +TEST_CASE("add_prefix_to_header", "[fastq::fastq]") +{ + const fastq expected("not_my_header", "ACGTA", "12345"); + fastq record("my_header", "ACGTA", "12345"); + record.add_prefix_to_header("not_"); + REQUIRE(record == expected); +} + + +TEST_CASE("add_prefix_to_header__empty_prefix", "[fastq::fastq]") +{ + const fastq expected("my_header", "ACGTA", "12345"); + fastq record = expected; + record.add_prefix_to_header(""); + REQUIRE(record == expected); +} + + +TEST_CASE("add_prefix_to_header__header", "[fastq::fastq]") +{ + const fastq expected("new_header", "ACGTA", "12345"); + fastq record("", "ACGTA", "12345"); + record.add_prefix_to_header("new_header"); + REQUIRE(record == expected); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Adding postfixes to the header + +TEST_CASE("add_postfix_to_header", "[fastq::fastq]") +{ + const fastq expected("my_header new postfix", "ACGTA", "12345"); + fastq record("my_header", "ACGTA", "12345"); + record.add_postfix_to_header(" new postfix"); + REQUIRE(record == expected); +} + + +TEST_CASE("add_postfix_to_header__empty_prefix", "[fastq::fastq]") +{ + const fastq expected("my_header", "ACGTA", "12345"); + fastq record = expected; + record.add_postfix_to_header(""); + REQUIRE(record == expected); +} + + +TEST_CASE("add_postfix_to_header__header", "[fastq::fastq]") +{ + const fastq expected("new_header", "ACGTA", "12345"); + fastq record("", "ACGTA", "12345"); + record.add_postfix_to_header("new_header"); + REQUIRE(record == expected); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Discarding read, setting seq to N and qual to '!' + +TEST_CASE("discard_read", "[fastq::fastq]") +{ + const fastq expected("my_header", "N", "!"); + fastq record("my_header", "ACGTA", "12345"); + record.discard(); + REQUIRE(record == expected); +} + + +TEST_CASE("discard_discarded_read", "[fastq::fastq]") +{ + const fastq expected("my_header", "N", "!"); + fastq record("my_header", "N", "!"); + record.discard(); + REQUIRE(record == expected); +} + + +TEST_CASE("discard_empty_read", "[fastq::fastq]") +{ + const fastq expected("my_header", "N", "!"); + fastq record("my_header", "", ""); + record.discard(); + REQUIRE(record == expected); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Reading from stream + +TEST_CASE("simple_fastq_record_1", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back("ACGAGTCA"); + lines.push_back("+"); + lines.push_back("!7BF8DGI"); + vec_reader reader(lines); + + fastq record; + CHECK(record.read(reader, FASTQ_ENCODING_33)); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); +} + +TEST_CASE("simple_fastq_record_2", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back("ACGAGTCA"); + lines.push_back("+"); + lines.push_back("!7BF8DGI"); + lines.push_back("@record_2"); + lines.push_back("GTCAGGAT"); + lines.push_back("+"); + lines.push_back("D7BIG!F8"); + vec_reader reader(lines); + + fastq record; + CHECK(record.read(reader, FASTQ_ENCODING_33)); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); + CHECK(record.read(reader, FASTQ_ENCODING_33)); + REQUIRE(record.header() == "record_2"); + REQUIRE(record.sequence() == "GTCAGGAT"); + REQUIRE(record.qualities() == "D7BIG!F8"); + CHECK(!record.read(reader, FASTQ_ENCODING_33)); +} + + +TEST_CASE("simple_fastq_record__with_extra_header_1", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1 Extra header here"); + lines.push_back("ACGAGTCA"); + lines.push_back("+"); + lines.push_back("!7BF8DGI"); + vec_reader reader(lines); + + fastq record; + CHECK(record.read(reader, FASTQ_ENCODING_33)); + REQUIRE(record.header() == "record_1 Extra header here"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); + CHECK(!record.read(reader, FASTQ_ENCODING_33)); +} + + +TEST_CASE("simple_fastq_record__with_extra_header_2", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back("ACGAGTCA"); + lines.push_back("+Extra header here"); + lines.push_back("!7BF8DGI"); + vec_reader reader(lines); + + fastq record; + CHECK(record.read(reader, FASTQ_ENCODING_33)); + REQUIRE(record.header() == "record_1"); + REQUIRE(record.sequence() == "ACGAGTCA"); + REQUIRE(record.qualities() == "!7BF8DGI"); + CHECK(!record.read(reader, FASTQ_ENCODING_33)); +} + + +TEST_CASE("simple_fastq_record__no_header", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@"); + lines.push_back("ACGAGTCA"); + lines.push_back("+"); + lines.push_back("!7BF8DGI"); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); +} + + +TEST_CASE("simple_fastq_record__no_sequence", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back(""); + lines.push_back("+"); + lines.push_back("!7BF8DGI"); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); +} + + +TEST_CASE("simple_fastq_record__no_qualities", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@"); + lines.push_back("ACGAGTCA"); + lines.push_back("+"); + lines.push_back(""); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); +} + + +TEST_CASE("simple_fastq_record__no_qualities_or_sequence", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@"); + lines.push_back(""); + lines.push_back("+"); + lines.push_back(""); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader, FASTQ_ENCODING_33), fastq_error); +} + + +TEST_CASE("eof_when_starting_to_read_record", "[fastq::fastq]") +{ + string_vec lines; + vec_reader reader(lines); + + fastq record; + CHECK(!record.read(reader)); +} + + +TEST_CASE("eof_after_header", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record"); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_sequence_1", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record"); + lines.push_back("ACGTA"); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_sequence_2", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record"); + lines.push_back("ACGTA"); + lines.push_back(""); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_sep_1", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record"); + lines.push_back("ACGTA"); + lines.push_back("+"); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_sep_2", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record"); + lines.push_back("ACGTA"); + lines.push_back("+"); + lines.push_back(""); + vec_reader reader(lines); + + fastq record; + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_qualities_following_previous_read_1", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back("ACGTA"); + lines.push_back("+"); + lines.push_back("!!!!!"); + lines.push_back("@record_2"); + lines.push_back("ACGTA"); + lines.push_back("+"); + vec_reader reader(lines); + + fastq record; + REQUIRE_NOTHROW(record.read(reader)); + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + + +TEST_CASE("eof_after_qualities_following_previous_read_2", "[fastq::fastq]") +{ + string_vec lines; + lines.push_back("@record_1"); + lines.push_back("ACGTA"); + lines.push_back("+"); + lines.push_back("!!!!!"); + lines.push_back("@record_2"); + lines.push_back("ACGTA"); + lines.push_back("+"); + lines.push_back(""); + vec_reader reader(lines); + + fastq record; + REQUIRE_NOTHROW(record.read(reader)); + REQUIRE_THROWS_AS(record.read(reader), fastq_error); +} + +/////////////////////////////////////////////////////////////////////////////// +// Writing to stream + +TEST_CASE("Writing_to_stream_phred_33", "[fastq::fastq]") +{ + const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); + REQUIRE(record.to_str() == "@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n"); +} + +TEST_CASE("Writing_to_stream_phred_33_explicit", "[fastq::fastq]") +{ + const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); + REQUIRE(record.to_str() == "@record_1\nACGTACGATA\n+\n!$#$*68CGJ\n"); +} + +TEST_CASE("Writing_to_stream_phred_64_explicit", "[fastq::fastq]") +{ + const fastq record = fastq("record_1", "ACGTACGATA", "!$#$*68CGJ"); + REQUIRE(record.to_str(FASTQ_ENCODING_64) == "@record_1\nACGTACGATA\n+\n@CBCIUWbfi\n"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Validating pairs + +TEST_CASE("validate_paired_reads__throws_if_order_or_number_is_wrong", "[fastq::fastq]") +{ + const fastq ref_mate0 = fastq("Mate/0", "ACGT", "!!#$"); + const fastq ref_mate1 = fastq("Mate/1", "ACGT", "!!#$"); + const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); + const fastq ref_mate3 = fastq("Mate/3", "ACGT", "!!#$"); + const fastq ref_matea = fastq("Mate/A", "ACGT", "!!#$"); + const fastq ref_mateb = fastq("Mate/B", "ACGT", "!!#$"); + + { + fastq mate0 = ref_mate0; + fastq mate1 = ref_mate1; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate0, mate1), fastq_error); + } + + { + fastq mate0 = ref_mate0; + fastq mate1 = ref_mate1; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate0), fastq_error); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + fastq::validate_paired_reads(mate1, mate2); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); + } + + { + fastq mate2 = ref_mate2; + fastq mate3 = ref_mate3; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate3), fastq_error); + } + + { + fastq mate2 = ref_mate2; + fastq mate3 = ref_mate3; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate3, mate2), fastq_error); + } + + { + fastq matea = ref_matea; + fastq mateb = ref_mateb; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(matea, mateb), fastq_error); + } + + { + fastq matea = ref_matea; + fastq mateb = ref_mateb; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mateb, matea), fastq_error); + } +} + + +TEST_CASE("validate_paired_reads__allows_other_separators", "[fastq::fastq]") +{ + const fastq ref_mate1 = fastq("Mate:1", "ACGT", "!!#$"); + const fastq ref_mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + fastq::validate_paired_reads(mate1, mate2, ':'); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); + } +} + + +TEST_CASE("validate_paired_reads__mate_separator_is_updated", "[fastq::fastq]") +{ + const fastq ref_mate_1 = fastq("Mate/1", "ACGT", "!!#$"); + const fastq ref_mate_2 = fastq("Mate/2", "GCTAA", "$!@#$"); + + fastq mate1 = fastq("Mate:1", "ACGT", "!!#$"); + fastq mate2 = fastq("Mate:2", "GCTAA", "$!@#$"); + fastq::validate_paired_reads(mate1, mate2, ':'); + + REQUIRE(ref_mate_1 == mate1); + REQUIRE(ref_mate_2 == mate2); +} + + +TEST_CASE("validate_paired_reads__throws_if_mate_is_empty", "[fastq::fastq]") +{ + const fastq ref_mate1 = fastq("Mate", "", ""); + const fastq ref_mate2 = fastq("Mate", "ACGT", "!!#$"); + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate1), fastq_error); + } +} + + +TEST_CASE("validate_paired_reads__throws_if_only_mate_1_is_numbered", "[fastq::fastq]") +{ + const fastq ref_mate2 = fastq("Mate/1", "GCTAA", "$!@#$"); + const fastq ref_mate1 = fastq("Mate", "ACGT", "!!#$"); + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); + } +} + + +TEST_CASE("validate_paired_reads__throws_if_only_mate_2_is_numbered", "[fastq::fastq]") +{ + const fastq ref_mate1 = fastq("Mate", "GCTAA", "$!@#$"); + const fastq ref_mate2 = fastq("Mate/2", "ACGT", "!!#$"); + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); + } + + { + fastq mate1 = ref_mate1; + fastq mate2 = ref_mate2; + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate2, mate1), fastq_error); + } +} + + +TEST_CASE("validate_paired_reads__throws_if_mate_is_misnumbered", "[fastq::fastq]") +{ + fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); + fastq mate2 = fastq("Mate/3", "ACGT", "!!#$"); + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); +} + + +TEST_CASE("validate_paired_reads__throws_if_same_mate_numbers", "[fastq::fastq]") +{ + fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); + fastq mate2 = fastq("Mate/1", "ACGT", "!!#$"); + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); +} + + +TEST_CASE("validate_paired_reads__throws_if_name_differs", "[fastq::fastq]") +{ + fastq mate1 = fastq("Mate/1", "GCTAA", "$!@#$"); + fastq mate2 = fastq("WrongName/2", "ACGT", "!!#$"); + REQUIRE_THROWS_AS(fastq::validate_paired_reads(mate1, mate2), fastq_error); +} + +} // namespace ar diff -Nru adapterremoval-2.2.2/tests/unit/main_test.cpp adapterremoval-2.2.3/tests/unit/main_test.cpp --- adapterremoval-2.2.2/tests/unit/main_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/main_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,2 @@ +#define CATCH_CONFIG_MAIN +#include "catch.hpp" diff -Nru adapterremoval-2.2.2/tests/unit/strutils_test.cpp adapterremoval-2.2.3/tests/unit/strutils_test.cpp --- adapterremoval-2.2.2/tests/unit/strutils_test.cpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/strutils_test.cpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,195 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#include +#include + +#include "testing.hpp" +#include "strutils.hpp" + +namespace ar +{ + +/////////////////////////////////////////////////////////////////////////////// +// Tests for 'toupper' + +TEST_CASE("ASCII letters are uppercased", "[strutils::toupper]") +{ + REQUIRE(toupper("") == ""); + REQUIRE(toupper("a1{2BZ`zAdeK") == "A1{2BZ`ZADEK"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Tests for 'indent_lines' + +TEST_CASE("Empty lines are not indented", "[strutils::indent_lines]") +{ + REQUIRE(indent_lines("") == ""); + REQUIRE(indent_lines("\n") == "\n"); + REQUIRE(indent_lines("\n\n") == "\n\n"); + REQUIRE(indent_lines("\n\n\n") == "\n\n\n"); +} + + +TEST_CASE("Singular lines are indented", "[strutils::indent_lines]") +{ + REQUIRE(indent_lines("this is a test") == " this is a test"); + REQUIRE(indent_lines("this is a test\n") == " this is a test\n"); +} + + +TEST_CASE("Multiple lines are indented", "[strutils::indent_lines]") +{ + REQUIRE(indent_lines("this is a test\nline #2") + == " this is a test\n line #2"); + REQUIRE(indent_lines("this is a test\nline #2\n") + == " this is a test\n line #2\n"); +} + + +TEST_CASE("Mixed lines are partially indented", "[strutils::indent_lines]") +{ + REQUIRE(indent_lines("this is a test\nline #2\n\n") + == " this is a test\n line #2\n\n"); + REQUIRE(indent_lines("this is a test\n\nline #2\n") + == " this is a test\n\n line #2\n"); + REQUIRE(indent_lines("this is a test\nline #2\n\n\n") + == " this is a test\n line #2\n\n\n"); +} + + +/////////////////////////////////////////////////////////////////////////////// +// Tests for 'columnize_text' + +TEST_CASE("Whitespace only is stripped", "[strutils::columnize_text]") +{ + REQUIRE(columnize_text("") == ""); + REQUIRE(columnize_text(" ") == ""); + REQUIRE(columnize_text("\n") == ""); + REQUIRE(columnize_text("\n\n") == ""); + REQUIRE(columnize_text("\n \n") == ""); + REQUIRE(columnize_text("\n ") == ""); + REQUIRE(columnize_text(" \n") == ""); + REQUIRE(columnize_text(" \n ") == ""); +} + + +TEST_CASE("Whitespace between words is stripped", "[strutils::columnize_text]") +{ + REQUIRE(columnize_text("foo bar") == "foo bar"); + REQUIRE(columnize_text("foo bar") == "foo bar"); + REQUIRE(columnize_text("foo\nbar") == "foo bar"); + REQUIRE(columnize_text("foo\nbar\n") == "foo bar"); + REQUIRE(columnize_text("\nfoo\nbar") == "foo bar"); + REQUIRE(columnize_text("foo\nbar\n\n") == "foo bar"); + REQUIRE(columnize_text("\nfoo\nbar\n") == "foo bar"); + REQUIRE(columnize_text("\n \n foo \n bar \n") == "foo bar"); +} + + +TEST_CASE("Linebreaks are added by max width", "[strutils::columnize_text]") +{ + REQUIRE(columnize_text("foo bar\nzood", 12) == "foo bar zood"); + REQUIRE(columnize_text("foo bar\nzood", 11) == "foo bar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 7) == "foo bar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 6) == "foo\nbar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 3) == "foo\nbar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 1) == "foo\nbar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 0) == "foo\nbar\nzood"); +} + + +TEST_CASE("Subsequent lines are indented", "[strutils::columnize_text]") +{ + REQUIRE(columnize_text("foo bar\nzood", 12, 2) == "foo bar zood"); + REQUIRE(columnize_text("foo bar\nzood", 11, 0) == "foo bar\nzood"); + REQUIRE(columnize_text("foo bar\nzood", 11, 1) == "foo bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 11, 2) == "foo bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 7, 2) == "foo bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 6, 2) == "foo\n bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 3, 2) == "foo\n bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 1, 2) == "foo\n bar\n zood"); + REQUIRE(columnize_text("foo bar\nzood", 0, 2) == "foo\n bar\n zood"); +} + + +TEST_CASE("Proper numbers are converted", "[strutils::str_to_unsigned]") +{ + REQUIRE(str_to_unsigned("0") == 0); + REQUIRE(str_to_unsigned("1") == 1); + REQUIRE(str_to_unsigned("2") == 2); + REQUIRE(str_to_unsigned("2147483647") == 2147483647); + REQUIRE(str_to_unsigned("2147483648") == 2147483648); + REQUIRE(str_to_unsigned("2147483649") == 2147483649); + REQUIRE(str_to_unsigned("4294967293") == 4294967293); + REQUIRE(str_to_unsigned("4294967294") == 4294967294); + REQUIRE(str_to_unsigned("4294967295") == 4294967295); +} + + +TEST_CASE("Whitespace is ignored", "[strutils::str_to_unsigned]") +{ + REQUIRE(str_to_unsigned(" 123") == 123); + REQUIRE(str_to_unsigned("123 ") == 123); + REQUIRE(str_to_unsigned(" 123 ") == 123); + REQUIRE(str_to_unsigned("\n123\n") == 123); +} + + +TEST_CASE("Numbers outside range are rejected", "[strutils::str_to_unsigned]") +{ + REQUIRE_THROWS_AS(str_to_unsigned("-2"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("-1"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("4294967296"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("4294967297"), std::invalid_argument); +} + + +TEST_CASE("Non numeric strings are rejected", "[strutils::str_to_unsigned]") +{ + REQUIRE_THROWS_AS(str_to_unsigned(" "), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("x"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("a b c"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("\n"), std::invalid_argument); +} + + +TEST_CASE("Mixed strings are rejected", "[strutils::str_to_unsigned]") +{ + REQUIRE_THROWS_AS(str_to_unsigned("1a"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("123x"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("123 x"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("x123"), std::invalid_argument); + REQUIRE_THROWS_AS(str_to_unsigned("x 123"), std::invalid_argument); +} + + +TEST_CASE("Base 10 is assumed", "[strutils::str_to_unsigned]") +{ + REQUIRE(str_to_unsigned("010") == 10); +} + + +} // namespace ar diff -Nru adapterremoval-2.2.2/tests/unit/testing.hpp adapterremoval-2.2.3/tests/unit/testing.hpp --- adapterremoval-2.2.2/tests/unit/testing.hpp 1970-01-01 00:00:00.000000000 +0000 +++ adapterremoval-2.2.3/tests/unit/testing.hpp 2019-01-22 21:39:48.000000000 +0000 @@ -0,0 +1,45 @@ +/*************************************************************************\ + * AdapterRemoval - cleaning next-generation sequencing reads * + * * + * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk * + * Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com * + * * + * If you use the program, please cite the paper: * + * S. Lindgreen (2012): AdapterRemoval: Easy Cleaning of Next Generation * + * Sequencing Reads, BMC Research Notes, 5:337 * + * http://www.biomedcentral.com/1756-0500/5/337/ * + * * + * This program is free software: you can redistribute it and/or modify * + * it under the terms of the GNU General Public License as published by * + * the Free Software Foundation, either version 3 of the License, or * + * (at your option) any later version. * + * * + * This program is distributed in the hope that it will be useful, * + * but WITHOUT ANY WARRANTY; without even the implied warranty of * + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * + * GNU General Public License for more details. * + * * + * You should have received a copy of the GNU General Public License * + * along with this program. If not, see . * +\*************************************************************************/ +#ifndef TESTING_H +#define TESTING_H + +#include + +#include "catch.hpp" +#include "fastq.hpp" + + +namespace ar { + +inline std::ostream& operator<<(std::ostream& stream, const fastq& record) +{ + return stream << "'@" << record.header() << "\\n" + << record.sequence() << "\\n+\\n" + << record.qualities() << "\\n'"; +} + +} + +#endif \ No newline at end of file diff -Nru adapterremoval-2.2.2/.travis.yml adapterremoval-2.2.3/.travis.yml --- adapterremoval-2.2.2/.travis.yml 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/.travis.yml 2019-01-22 21:39:48.000000000 +0000 @@ -15,17 +15,20 @@ packages: - zlib1g-dev - libbz2-dev + - python3 + - python3-pip before_install: - - pip install --user cpp-coveralls + - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then python3 -m pip install --user cpp-coveralls; fi install: true script: - make - - make test COVERAGE=yes - - make validate + - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make test COVERAGE=yes; fi + - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make test COVERAGE=no; fi + - make regression - PATH=$PATH:$PWD/build/ make -C examples after_success: - - coveralls --exclude tests --exclude googletest-release-1.8.0 --gcov-options '\-lp' + - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then python3 -m coveralls --exclude tests --gcov-options '\-lp'; fi diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 TGAGTCAT GTTAGTGG -sample_2 GCAGAGAT CCTAGGGT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -GCAGAGATACCCTAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -GCAGAGATCCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTACACCCTAGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -TGAGTCATCCACTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -TGAGTCATGCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACCCCACTAACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TGAGTCATACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -GCAGAGATGCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGAGTCATAGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -GCAGAGATTAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -CCTAGGGTATCTCTGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -CCTAGGGTGTACCGACAAGCCATTAAGTCAACTCAGCGGAAGTCGTCGGGACGATGCCCAAACGCGCACTTAACTTTTGTAGGATCTCTGCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -GTTAGTGGATGACTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTTAGTGGGGTGATGATATCAGGAGCCGTATTCTAAAGTGATTAGACAATTACATGGACAGACAAACGGCAGTGTAACTGTGCATGACTCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -GTTAGTGGGATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -CCTAGGGTTTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTTAGTGGATGTGGTTATAGCAACCGCTCACTTCTCACGTACTGGTGATACTCCTTTGGTACTTTCAACCGTTTTTCCTTTTACGAGATAATCTGGATGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -CCTAGGGTCCTCTCGATTCGGCAGTACCCAATTGTTGACGATCAGCATATTATTATCTGATTGTGCTCGGCGCCCTACATTTCGCGTTGGAGTGTACGCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_read_s1_075 -GCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACC -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ -@M_read_s1_150 -AGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTTGAAAGTACCAAAGGAGTATCACCAGTACGTGAGAAGTGAGCGGTTGCTATAACCACAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_000 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_200/1 -ACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_200/2 -GATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,208 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* TGAGTCAT GTTAGTGG -sample_2 GCAGAGAT CCTAGGGT - - -[Adapter sequences] -Adapter1[1]: CCACTAAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGACTCA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4078236736 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of full-length collapsed pairs: 2 -Number of truncated collapsed pairs: 0 -Number of retained reads: 4 -Number of retained nucleotides: 409 -Average length of retained reads: 102.25 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 1 0 0 1 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 1 1 0 0 0 0 2 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 0 0 0 0 0 0 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_read_s2_075 -CCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTAC -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ -@M_read_s2_150 -TAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGAGCACAATCAGATAATAATATGCTGATCGTCAACAATTGGGTACTGCCGAATCGAGAGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_000 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_200/1 -GCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_200/2 -TTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,208 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TGAGTCAT GTTAGTGG -sample_2* GCAGAGAT CCTAGGGT - - -[Adapter sequences] -Adapter1[1]: ACCCTAGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATCTCTGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4078236736 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of full-length collapsed pairs: 2 -Number of truncated collapsed pairs: 0 -Number of retained reads: 4 -Number of retained nucleotides: 409 -Average length of retained reads: 102.25 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 1 0 0 1 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 1 1 0 0 0 0 2 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 0 0 0 0 0 0 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TGAGTCAT GTTAGTGG -sample_2 GCAGAGAT CCTAGGGT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 TGAGTCAT GTTAGTGG 4 0.500 -sample_2 GCAGAGAT CCTAGGGT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -N -+ -! diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -N -+ -! diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -N -+ -! -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/2 -N -+ -! -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/combined_output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_150/1 -TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2* AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GGCCCCTG CCAAAGCT 4 0.500 -sample_2 AATCCTAG GTCTAGTT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GTCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_150/1 -TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_150/2 -TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -TACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/2 -CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2* AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GGCCCCTG CCAAAGCT 4 0.500 -sample_2 AATCCTAG GTCTAGTT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -GTCTAGTTCTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -CCAAAGCTTTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -GTCTAGTTAAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GTCTAGTTGACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CCAAAGCTCAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -CCAAAGCTGCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_150/1 -TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_150/2 -TTTAGACGGCAGACGCATCAACTTCCACATGACTGCTTGAACGACGATACACCTCTATATATACAACGACATTATGCGAAAGCGCTAATGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CAGGGGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GCGTCGAGGCACGAACATGGGTGATTGAGGGAGGCTGTTCTTTGTTCTAGCGGAGTTTTTCCCTACATAGCCACCCAGGGGCCAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_000/1 -AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_000/2 -CTAGGATTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -AAGCCAGTGCCCGCAAGTGGTACCTCCTTTATGGTACACCGAACACAGCGCTTCGCCTGGCTCAAACTGCAGCAGCAAGTACCTGCTCGATG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GACTGAGGGGCGCATTCTTAGTCGAGTCGTTTGTGGATAGTCAGGTCTGGTAAAGGATGTACCGGGATGCTCGTACCGAGGCAGGAGTGTTT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2* AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 2 0.250 -ambiguous NA NA 0 0.000 -sample_1 GGCCCCTG CCAAAGCT 3 0.375 -sample_2 AATCCTAG GTCTAGTT 3 0.375 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_200/1 -TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_200/2 -CCAAAGCTTACGGGTCCGTGCGCTTAGGTAAGAGCCCCGTTTTTTACGCGGAAAAGCGCCTGGAAGCTCAGAATTGAGGGAAGGGAAATGAGTCACGGGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -ATCTAGTTGAAACGTAGCGCAATCGGGTACGATTTACGATGGCCTGTACACCGAGAGTTGCAGTTCCAGGACGCACAGCGTATCTAGGATTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 TTTTCAAC TAGATGGC -sample_2 CTTTACAG GGGCTGCT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,64 +0,0 @@ -@read_s2_000/1 -CTTTACAGAGCAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -GGGCTGCTCTGTAAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TTTTCAACTTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -TAGATGGCGTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CTTTACAGCCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -GGGCTGCTAATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -TTTTCAACTCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCAGCCATCTAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -TAGATGGCTGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGAGTTGAAAAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CTTTACAGCCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGCAGCAGCCCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GGGCTGCTGCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGGCTGTAAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -TTTTCAACGCCATCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -TAGATGGCGTTGAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CTTTACAGTTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GGGCTGCTGTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TTTTCAACCAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -TAGATGGCTAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s1_150/1 -TTGACTTACACCCAGACGCTTCCGAACGAGGGGACGTGGCAAAGCGACAATCCTGTCAACACTATAATGCTTCCGAACGCAATATAAAGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTACTTTACGAGATTGAGTGGATGAATCGGCGTTGCCCAAGCAGAGGCTCGGCTTTCGTTCCTTTATATTGCGTTCGGAAGCATTATAGTGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -TCGATATCTTTTGAGCAGGGATGCTTCCAGCACGTGAACCCAGGAAAATGCACGCGCGCGCACTGCACCCCCCCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_075/2 -TGGGGGGGTGCAGTGCGCGCGCGTGCATTTTCCTGGGTTCACGTGCTGGAAGCATCCCTGCTCAAAAGATATCGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -CAGGGTGGTGAACTACTCGTCCCATTCTTATCGCCGTCTTAACTCGGGACAGTAGTGCTCGAATCGCTCGCGGGGCTCCTCGGCCTTCAATG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -TAACTGGACGGTGACATTCTGCCGGTACCTAGACTGATCTTAAAACAGCCCGCACTCCGTATGTTCTAGGACAAGGTGGCATCTAGAACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* TTTTCAAC TAGATGGC -sample_2 CTTTACAG GGGCTGCT - - -[Adapter sequences] -Adapter1[1]: GCCATCTA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: GTTGAAAA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s2_200/1 -CCTAATAACTTGTTAATGACATCCTAAGCCCTTTGAAAAACTTTTCGTTGGATACGGTCCAGTCAGAAACTTTCAAAATCGGCCCGGGCGCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -AATACCCCTTAGTGTAGCTGGCGACTTCATCCAGACTGTATGTCTCTAGAGTTCATAACTCCGCGCACCGTCAACGTCTGATCATGCTGGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CCTGGAATCGCTGGTTACGGATGGTATTTAGATTATGGTACATCTAACAACATATGTCACACATTCCGGATCGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_075/2 -GCCGATCCGGAATGTGTGACATATGTTGTTAGATGTACCATAATCTAAATACCATCCGTAACCAGCGATTCCAGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -TTAGCGCTTTTGCGCCGACTCATGAGTTTAGGGGAGGGATCTCACTCTACCCGACTACGGGCTCGAGTATCCGATACTTGCACAGATGAATA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GTGGTTGGTCGAATATCCTGACTACCAACTCCTGGTACAATGGAGAATCTGACGGTGGTATTCATCTGTGCAAGTATCGGATACTCGAGCCC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TTTTCAAC TAGATGGC -sample_2* CTTTACAG GGGCTGCT - - -[Adapter sequences] -Adapter1[1]: AGCAGCCC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTGTAAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TTTTCAAC TAGATGGC -sample_2 CTTTACAG GGGCTGCT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 TTTTCAAC TAGATGGC 4 0.500 -sample_2 CTTTACAG GGGCTGCT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 TGTAACGC CTCCTTAG -sample_2 GGGGACTC GTATATGC diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_150/1 -TGTAACGCGAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -TGTAACGCCTAAGGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -GGGGACTCAAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGGGCATATACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -GGGGACTCGCATATACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TGTAACGCCCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -TGTAACGCTGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCCCTAAGGAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -GGGGACTCCATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -GGGGACTCATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_150/2 -CTCCTTAGTGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CTCCTTAGGCGTTACAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -GTATATGCCCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTTGAGTCCCCAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -GTATATGCGAGTCCCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CTCCTTAGGTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -CTCCTTAGGGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCAGCGTTACAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -GTATATGCCGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -GTATATGCAGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s1_150/1 -GAAAGCTTGCCAACTCTCAGATTACAGTTTAGCAATTCTCCGATAGACGTAGATAATAGTTGCGTTGACCGCTTTTCGGGGCACGGAAGTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -TGGATGGGCAGAGAGATTCCCATTTGGCAGCGAGCGAGCCCCGTAGATAGCTGCTCTCTGACTTCCGTGCCCCGAAAAGCGGTCAACGCAAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CCAGCATCAAACATAACGTGATAGATACTCAACCATTTTCGGAGTAAACAATGAGAATAACCATGCGGCATGGGACGTGACACCAACGAACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -GTCCGAGCGCTAGGACCAGTCCCGTGTACCCAAATAGCGCGACCCCGTCCACGGTGTATGGGCAGTTACGGTAATCTTATGTTCAAAATGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -TGATGTGGCTCTAAAAGACCGGACGTTTCGCGTCCTTTGGAGCGGGTAGTGCGGTAGTAAAAATTTACACTAGCC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_075/2 -GGCTAGTGTAAATTTTTACTACCGCACTACCCGCTCCAAAGGACGCGAAACGTCCGGTCTTTTAGAGCCACATCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* TGTAACGC CTCCTTAG -sample_2 GGGGACTC GTATATGC - - -[Adapter sequences] -Adapter1[1]: CTAAGGAG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: GCGTTACA_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s2_075/1 -AAGAATCCGAGGCATAGCGAATCAATGTCACTTTGGTTCTGTCAGAACGACCTGCGAATCAAAACATGCCACGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_075/2 -CCCGTGGCATGTTTTGATTCGCAGGTCGTTCTGACAGAACCAAAGTGACATTGATTCGCTATGCCTCGGATTCTT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -CATTAGCCCACGCAACGGCTTAGGCGTCGAGGACATTAACAAGGGCGCGAGGGCCTTCACTTACATGGTATCTATCTCATCCAGTGCACGAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -CGAACTAGGTAGTCGCTTTACATAGGAGAGGTCGTTATGTATTACGTCACCGCGTTTCGTCGTGCACTGGATGAGATAGATACCATGTAAGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -ATCTCAAGCTCAAGATTAGCAGAAGGATTGTAGGCCCGGATCCGATAATCGATAAAGCCGTGATGTCAATACGGTCCCGGTCTGTCCAGCTA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -AGATGCAGTACTGATTGAGAACTTTCAAATAACCCAAACAAGCGTACCAATGTATACTAGCCCACCGGCCTTCATCATCTAATTAATAGCAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TGTAACGC CTCCTTAG -sample_2* GGGGACTC GTATATGC - - -[Adapter sequences] -Adapter1[1]: GCATATAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: GAGTCCCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 TGTAACGC CTCCTTAG -sample_2 GGGGACTC GTATATGC - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 TGTAACGC CTCCTTAG 4 0.500 -sample_2 GGGGACTC GTATATGC 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/2 -TGCACGGGCATCGGCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -TGCACGGGTAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -ACGTTATTTCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACCAGGGCAAGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ACGTTATTAAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ACGTTATTGTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGCACGGGTGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGACATCGGCGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -TGCACGGGAAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -ACGTTATTAGGGCAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -TCATCCTGTCTAATTATACCAATGCAGGAACGGGGGCCAAGATCCCCTCGTCCACCTGATGGAGAACGTAGAACC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/2 -AAGGCCCGCCCATCAGGTAAGAGCATGCTCGGGAGCCAACCCCGTGGGGTGGCAGCGATACTCTCCAATCTGTCATGCGTGTCAACGTGCGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -GTGCTGCGTGAGTTGGAAGGATTGGATCCGGAAAGGCTTGGCCTTTGTAAATTCGACTGCGAGTGCGTTGGGCCGGTATACCAGGTAGAGGG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/2 -TAAGGGACGAAGTCACCGGGGGCGTTTCACTTGCGCGATCCATTGTAGTACTGGTGTGTCAATCTTCATCGGCAAAAGGTGCCTATCAAAAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGTCCCGTCCTATTGCGGTGGTTTGGGACGTCTCGATATCCATCACTTTAATTGGTGGCACTCTCGTTCCCAAGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/2 -AAGGCTGGGTATACGGGGTAAATGGTGCCGCCTTGTTACACGCGCCGAGGTTTCAGATGAGAGAGTTGTCTTTATTCCCTTCTAGCCACGAG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,148 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 518 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 2 0 0 4 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/pe/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/pe/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,147 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 935224950 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 2 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 1 1 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 1 0 0 1 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,147 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 935224950 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 2 -Number of reads with adapters[1]: 3 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 1 1 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 1 0 0 1 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 1 0 0 0 1 -92 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -N -+ -! diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -N -+ -! -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/combined_output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_150/1 -TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -AACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2* AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/regular/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,26 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GGCCCCTG CCAAAGCT 4 0.500 -sample_2 AATCCTAG GTCTAGTT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -AATCCTAGAACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GGCCCCTGTTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -AATCCTAGTCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -AATCCTAGATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -AATCCTAGATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -GGCCCCTGAGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGCCCCTGGGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_150/1 -TTTCTGGACGACGCCCCTATAATGTATGATAATTATTCGATTGACATGGCGAACTTCAGCCATTAGCGCTTTCGCATAATGTCGTTGTATAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -AGCTTTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GGTGGCTATGTAGGGAAAAACTCCGCTAGAACAAAGAACAGCCTCCCTCAATCACCCATGTTCGTGCCTCGACGCAGCTTTGGAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGCTTTGG_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CAGGGGCC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -AACTAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -TCGTACAATGCATCAGACACCGCTTTTGTGGCGTTTCGACCGTAATCTACATTTACATCTCGTTAATTCGCGACATTCATCGTGCCGTACTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -ATACGCTGTGCGTCCTGGAACTGCAACTCTCGGTGTACAGGCCATCGTAAATCGTACCCGATTGCGCTACGTTTCAACTAGACAGATCGGAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATACCCCGACACTCGACTTATATTTTCCTCAGCTAGTGCGAGAGTTAATGTAGCGACGAAACACTCCTGCCTCGGTACGAGCATCCCGGTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2* AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AACTAGAC_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTAGGATT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,26 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Demultiplexing of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GGCCCCTG CCAAAGCT -sample_2 AATCCTAG GTCTAGTT - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 1 0.125 -ambiguous NA NA 0 0.000 -sample_1 GGCCCCTG CCAAAGCT 3 0.375 -sample_2 AATCCTAG GTCTAGTT 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/demux_only/unidentified/your_output.unidentified.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_200/1 -TGCCCCTGAACCATCTGAGCGGTACTCGGGAAAACACGGACGAGGTGGGATATCTTTCCCTTCTCTTGCCATCGTGTATTTATCTGTATCTAATGCTACT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/info.json adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/info.json --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_000/1 -CGCCGATGCCCGTGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CGCCGATGGCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGATC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CTTGCCCTGGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGAAATAACGTAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CTTGCCCTGTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CTTGCCCTCAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CGCCGATGTCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACACCCGTGCAAGATCGGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CGCCGATGAGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CTTGCCCTAATAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AATAACGT_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGGGCAAG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4115144913 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GGTTCTACGTTCTCCATCAGGTGGACGAGGGGATCTTGGCCCCCGTTCCTGCATTGGTATAATTAGACAGGATGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -GTAGTGCAATAAAAGGATCCTCTTGTGGCCGATTGCAGACCAGCCTCGGGGCTAAACTGATAATCGTATGCTATAGACCCTGGTCGACGCCG -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAGATGTCAGCTCATGTGTTGATATACAGCTAACTAAGGCCCGGGGGTTTAGGCTCAACCCTCTACCTGGTATACCGGCCCAACGCACTCGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2* CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: CCCGTGCA_AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CATCGGCG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 356769071 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 1 -Number of well aligned reads: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 3 -Number of retained reads: 3 -Number of retained nucleotides: 258 -Average length of retained reads: 86 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 1 0 1 -92 1 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_200/1 -GCGTAAGTTGACGTCAGCCTGCGAGGTGCCACGCCAGTGGTTGCGCTCACCCGGGGCGTAGTTGCTCCGCGCAATTTCTTGGCAGTTCGAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::998876654321 -@read_s2_075/1 -TCTTGGGAACGAGAGTGCCACCAATTAAAGTGATGGATATCGAGACGTCCCAAACCACCGCAATAGGACGGGACA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_150/1 -AGCCCCGAGTGTCCATCACAAGCCACCTCCACTAACCATCTCGGTCCATTATTTGTCACTCGTGGCTAGAAGGGAATAAAGACAACTCTCTC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/double_indexed/se/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/double_indexed/se/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of double-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CTTGCCCT ACGTTATT -sample_2 CGCCGATG TGCACGGG - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CTTGCCCT ACGTTATT 4 0.500 -sample_2 CGCCGATG TGCACGGG 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 CAAGCACG -sample_2 ATTTTGAG diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_200/1 -ATTTTGAGCTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -ATTTTGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -ATTTTGAGGATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -CAAGCACGAAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -ATTTTGAGCTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTTAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/1 -CAAGCACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -CAAGCACGTCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -CAAGCACGTCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCGAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s2_200/2 -ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -CTCAAAATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -ACTATGGTTGTCTGAATCACAAATGGCTAAACGGCTTCATAATAGTGTGGTATGCGTACTAAGTCTGCGGTCCTCACGATGTCACTGTCTACTATTTAGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -AAGGGTTGTGTCAGGGAACCACGATTAGATTCCGTCACGCATGCCCTAAAATGACCAAGAGGAAGTCTTTTCAAGCTCAAAATAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -CGTGCTTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -TCGCGCGAACGGCGCTGGGCCCCATGCGAAAAAGCGATACCATGAAGCGAGTATAATGTTCATGCACAGCCGCGATCCGAGCGCCCCACTGCATTGACGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -CGGTTGGGAGCTAGGCATGGGCTGTCTACTTTGTCGTGCCGGGTACCATGTAGGAATTGCCCACCGAGACTACGACGTGCTTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_read_s1_150 -TCAATCCAAGGGATAAGCATGCGCCCATATAGTGGTAGCACAGCAATCTTCCGTCAATGCAGTGGGGCGCTCGGATCGCGGCTGTGCATGAACATTATACTCGCTTCATGGTATCGCTTTTTCGCATGGGGCCCAGCGCCGTTCGCGCGA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH -@M_read_s1_075 -TCGTAGTCTCGGTGGGCAATTCCTACATGGTACCCGGCACGACAAAGTAGACAGCCCATGCCTAGCTCCCAACCG -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_000 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_200/1 -AAGCGAGTCTCGGTTGCGTGTCTTAAAGACAAAGGGACTCCATACTGGCCGGAAGTCCGATATCGCTTAGTAACTCACTCTCGCAGTATTTA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_200/2 -ATTTCACTGCCGGTTTGCTGTTCGGAATTTCTGTGAATTCGTGATTGCCATTGGGGAGGTTAAGGCAAACTATGAGATTGTTCCGGGTCAAGTAACTGGG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,208 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* CAAGCACG * -sample_2 ATTTTGAG * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CGTGCTTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2769367494 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of full-length collapsed pairs: 2 -Number of truncated collapsed pairs: 0 -Number of retained reads: 4 -Number of retained nucleotides: 417 -Average length of retained reads: 104.25 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 1 0 0 1 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 1 0 0 0 0 0 1 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 1 0 0 0 0 1 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_read_s2_150 -GATCTAACTGGATCGAGATAGGGCTGAGTGTGGCCGACGTTTTTGCCGCCCCTAAATAGTAGACAGTGACATCGTGAGGACCGCAGACTTAGTACGCATACCACACTATTATGAAGCCGTTTAGCCATTTGTGATTCAGACAACCATAGT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGGHHHHHHHH -@M_read_s2_075 -CTTGAAAAGACTTCCTCTTGGTCATTTTAGGGCATGCGTGACGGAATCTAATCGTGGTTCCCTGACACAACCCTT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_000 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_200/1 -CTCAATAAGCTGTGCTAGAAGGAAGAGTCTAAGGCGACGACGACATTTGGCGTCGCCTCGCCGAGGCTAGTGATCTAGCTGGCAGTACCCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_200/2 -ACCTAATGCAAGTTCCTTGTGATGTTAGAATATCCTAAGTCTATGGAATTCTTTTGCTTGGGAATTGTTGGCCTAAGTAGGTGGGTCGCCTTAGCGTGAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,208 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CAAGCACG * -sample_2* ATTTTGAG * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: CTCAAAAT_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2769367494 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of full-length collapsed pairs: 2 -Number of truncated collapsed pairs: 0 -Number of retained reads: 4 -Number of retained nucleotides: 417 -Average length of retained reads: 104.25 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 1 0 0 1 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 1 0 0 0 0 0 1 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 1 0 0 0 0 1 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 CAAGCACG * -sample_2 ATTTTGAG * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 CAAGCACG * 4 0.500 -sample_2 ATTTTGAG * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/1 -N -+ -! -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/2 -N -+ -! -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -N -+ -! -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/2 -N -+ -! -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/combined_output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/1 -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.pair2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,19 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/demux_only/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/demux_only/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,64 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--thread", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/input_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/input_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/2 -TCCGGCGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/2 -ATGTCCTGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTCTCCGGCGCAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGAATGTCCTGAGATCGGAAGAGCGTCG -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 - -+ - -@read_s1_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/2 -GTAGGAGCTTAATGATTCATCTGTCGATTTATTCACGCAAATGTGTAAATCCGATAGTGCATTAATGGGACCGTC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s1_200/2 -CCTTCTTATGCTCGACTGGCTCTGTATAAGCCCAAGACATTATGAAAGGTCTCGCGTTTGTCTACCAGGCTCCGTTACGGATACAAGTGCCCTACTGTCA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/2 -ATCAAGGGAGGTCACGTGAATTTTGCCTTCTAGACTAGCGTACATGACCGCGAATTAGATACGTTATAACCTTGCATAGACTCTAGCGGCGTCAGTAATA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_000/1 - -+ - -@read_s2_000/2 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/2 -AGAACAGGATACAATGAAAATGCATCGCGTTGGCAACTCTCACCTTGCTCTTGGACCCGTGTGTAGCAGGTACAAGTAAAGACTCTGTTGCCTAGGTTAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/2 -TGAAATACCTATCTGAGAAACGCCCCGGTATGCACGCTCTAAAACGTCGCGGAAAGCGTGATCTTGGGCTAGCGA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>> -@read_s2_200/2 -ATGCTGATTAGATATGTCTTTCATCGGCTTGTGACCGAGGAGTGGTACGGCCGTTCCATATTGGGTGATTAGGAAGATGTCCCGGCTTGCTGCTTCTCGT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,156 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2459456692 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 4 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 3 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 4 -Number of retained reads: 6 -Number of retained nucleotides: 534 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 1 1 0 0 2 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 2 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/pe/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/pe/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-indexed paired-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 -Maximum mate 1 mismatches: 0 -Maximum mate 2 mismatches: 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1157297082 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,147 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3843883243 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 2 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 1 1 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 1 0 0 1 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,147 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3843883243 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 2 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 1 1 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 1 0 0 1 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 2 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/1 -N -+ -! -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -N -+ -! -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/combined_output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/combined_output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s1_000/1 -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_s2_000/1 -AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,17 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/demux_only/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/demux_only/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,26 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Demultiplexing of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/barcodes.txt adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/barcodes.txt --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/barcodes.txt 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/barcodes.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -sample_1 GCGCCGGA -sample_2 CAGGACAT diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/info.json adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/info.json --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/input_1.fastq adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,32 +0,0 @@ -@read_s1_000/1 -GCGCCGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_000/1 -CAGGACATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_075/1 -GCGCCGGAGACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTACAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_150/1 -CAGGACATTGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_200/1 -GCGCCGGATCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -GCGCCGGATGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -CAGGACATTCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCAAGATCGGAAGAGCACAC -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_200/1 -CAGGACATACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s1_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1* GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: TCCGGCGC_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s1_075/1 -GACGGTCCCATTAATGCACTATCGGATTTACACATTTGCGTGAATAAATCGACAGATGAATCATTAAGCTCCTAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s1_200/1 -TCCATCAGGATCGTATTATACTAAGCTAGGACTGTGCAGTGCACAGAGAGGAGATGACCATGATCCTCGAGCAAGTTGCCGCAGGCTCGGGC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s1_150/1 -TGCACCGTAGCCATATGGGCTGTTGGGGACACAGGGCGTCGGCATTCCTTTATTACTGACGCCGCTAGAGTCTATGCAAGGTTATAACGTAT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@read_s2_000/1 - -+ - diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2* CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: ATGTCCTG_AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 4 -Number of unaligned reads: 2 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 3 -Number of reads with adapters[1]: 2 -Number of retained reads: 3 -Number of retained nucleotides: 259 -Average length of retained reads: 86.3333 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 1 0 1 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 2 0 2 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.sample_2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,12 +0,0 @@ -@read_s2_150/1 -TGATCTCATACATTTAAACAAAGTATGCCTTACGCATGCCTTAATGATACGTAACCTAGGCAACAGAGTCTTTACTTGTACCTGCTACACAC -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 -@read_s2_075/1 -TCGCTAGCCCAAGATCACGCTTTCCGCGACGTTTTAGAGCGTGCATACCGGGGCGTTTCTCAGATAGGTATTTCA -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<; -@read_s2_200/1 -ACCCTCACGCTTGCACGACGACAGCGGTCCCCTATAAATGTATGTTGACGCAGCGAGAGGCCAGGACCCGGGCGTGTTACCACTAAGACCCT -+ -GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210 diff -Nru adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.settings adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/demultiplexing/single_indexed/se/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/demultiplexing/single_indexed/se/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-indexed single-end reads - - -[Demultiplexing] -Maximum mismatches (total): 0 - - -[Demultiplexing samples] -Name Barcode_1 Barcode_2 -sample_1 GCGCCGGA * -sample_2 CAGGACAT * - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3717807245 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Demultiplexing statistics] -Name Barcode_1 Barcode_2 Hits Fraction -unidentified NA NA 0 0.000 -ambiguous NA NA 0 0.000 -sample_1 GCGCCGGA * 4 0.500 -sample_2 CAGGACAT * 4 0.500 -* * * 8 1.000 diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/info.json adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": ["--demultiplex-only"], - "return_code": 1, - "stderr": [ - "Cannot use --demultiplex-only without specifying a list of barcodes using --barcode-list!" - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/input_1.fastq adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/input_1.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/input_2.fastq adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/input_2.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/demux_without_barcodes/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/demux_without_barcodes/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/info.json adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": [], - "return_code": 1, - "stderr": [ - "Error: Different number of files specified for --file1 and --file2." - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_1a.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_1a.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_1b.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_1b.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG -@read_150_3/2 -GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT -+ -HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_2b.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_2b.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_2b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/2 -TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA -+ -HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 -@read_150_7/2 -ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT -+ -HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_2c.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_2c.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file1/input_2c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file1/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_150_9/2 -GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT -+ -GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= -@read_150_10/2 -TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA -+ -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/info.json adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": [], - "return_code": 1, - "stderr": [ - "Error: Different number of files specified for --file1 and --file2." - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/input_1a.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/input_1a.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/input_1b.fastq adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/input_1b.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/fewer_file2/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/fewer_file2/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>E6,735@GG -@read_150_3/2 -GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT -+ -HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/file2_only/info.json adapterremoval-2.2.3/validation/misc/bad_args/file2_only/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/file2_only/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/file2_only/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": [], - "return_code": 1, - "stderr": [ - "Error: Different number of files specified for --file1 and --file2." - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/info.json adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": ["--identify-adapters", "--demultiplex-only"], - "return_code": 1, - "stderr": [ - "Cannot use --identify-adapters and --demultiplex-only at the same time!" - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/input_1.fastq adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/input_1.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/input_2.fastq adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/input_2.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/ident_and_demux/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/ident_and_demux/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/negative_window/info.json adapterremoval-2.2.3/validation/misc/bad_args/negative_window/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/negative_window/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/negative_window/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": ["--trimwindows", "-1"], - "return_code": 1, - "stderr": [ - "Error: Invalid value for --trimwindows" - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/negative_window/input_1.fastq adapterremoval-2.2.3/validation/misc/bad_args/negative_window/input_1.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/negative_window/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/negative_window/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500_1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500_2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved/info.json adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": ["--interleaved"], - "return_code": 1, - "stderr": [ - "Pair contains reads with mismatching names:" - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved/input_1.fastq adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved/input_1.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500_1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500_2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved_input/info.json adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved_input/info.json --- adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": ["--interleaved-input"], - "return_code": 1, - "stderr": [ - "Pair contains reads with mismatching names:" - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved_input/input_1.fastq adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved_input/input_1.fastq --- adapterremoval-2.2.2/validation/misc/bad_args/se_interleaved_input/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/bad_args/se_interleaved_input/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500_1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500_2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/misc/empty/pe/info.json adapterremoval-2.2.3/validation/misc/empty/pe/info.json --- adapterremoval-2.2.2/validation/misc/empty/pe/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/empty/pe/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/empty/pe/your_output.settings adapterremoval-2.2.3/validation/misc/empty/pe/your_output.settings --- adapterremoval-2.2.2/validation/misc/empty/pe/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/empty/pe/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 220897227 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 0 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All diff -Nru adapterremoval-2.2.2/validation/misc/empty/se/info.json adapterremoval-2.2.3/validation/misc/empty/se/info.json --- adapterremoval-2.2.2/validation/misc/empty/se/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/empty/se/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/misc/empty/se/your_output.settings adapterremoval-2.2.3/validation/misc/empty/se/your_output.settings --- adapterremoval-2.2.2/validation/misc/empty/se/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/empty/se/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,42 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2121675954 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 0 -Number of unaligned reads: 0 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All diff -Nru adapterremoval-2.2.2/validation/misc/no_arguments/info.json adapterremoval-2.2.3/validation/misc/no_arguments/info.json --- adapterremoval-2.2.2/validation/misc/no_arguments/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/misc/no_arguments/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,7 +0,0 @@ -{ - "arguments": [], - "return_code": 1, - "stderr": [ - "This program searches for" - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,146 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1203911406 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,146 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2579970730 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,146 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2579970730 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 1 1 0 0 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2644350168 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2806715714 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3115920885 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2416745148 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2644350168 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2806715714 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3115920885 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2543753157 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 108917414 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 108917414 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2294078498 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2378184469 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 99 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 1 0 1 -100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2394981856 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 99 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 1 0 1 -100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,87 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2027572855 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 1 1 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEE diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2010319782 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 1 1 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTAC -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEF diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2024298981 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 1 1 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCATN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCAT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220. diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 196 -Average length of retained reads: 98 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 1 0 0 1 -98 0 0 0 0 0 -99 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAA -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3198577441 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 198 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities", "--minquality", "31"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGCCTAGAATTTTTCGTTCGGTAAGCATTAGGAAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTAGCCCGTAGGGGCCTACAACGTTGGGGCCTTTGCGTAGTTGTATATAGC -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@BB diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/non_overlapping/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,112 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3418474566 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 31: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 1 -Number of well aligned read pairs: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 135 -Average length of retained reads: 67.5 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 1 0 0 0 1 -68 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/your_output.collapsed adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/your_output.collapsed --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/your_output.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_ATAGCCSeq_1_2959_500 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,196 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 664708214 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 150 -Average length of retained reads: 150 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 0 0 0 0 0 0 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,196 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1520646958 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 150 -Average length of retained reads: 150 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 0 0 0 0 0 0 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCACTACAAAAGAAAAACCCGGCTAGTGGTGGCAGCGATCGACAATCCAGATG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJCEBCEDECDEEEFFFFEFDGFIFFFHIIIGIHHGJGIGJJJIHJHJIIJHJ -@M_ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,196 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1520646958 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 150 -Average length of retained reads: 150 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 0 0 0 0 -51 0 0 0 0 0 0 0 -52 0 0 0 0 0 0 0 -53 0 0 0 0 0 0 0 -54 0 0 0 0 0 0 0 -55 0 0 0 0 0 0 0 -56 0 0 0 0 0 0 0 -57 0 0 0 0 0 0 0 -58 0 0 0 0 0 0 0 -59 0 0 0 0 0 0 0 -60 0 0 0 0 0 0 0 -61 0 0 0 0 0 0 0 -62 0 0 0 0 0 0 0 -63 0 0 0 0 0 0 0 -64 0 0 0 0 0 0 0 -65 0 0 0 0 0 0 0 -66 0 0 0 0 0 0 0 -67 0 0 0 0 0 0 0 -68 0 0 0 0 0 0 0 -69 0 0 0 0 0 0 0 -70 0 0 0 0 0 0 0 -71 0 0 0 0 0 0 0 -72 0 0 0 0 0 0 0 -73 0 0 0 0 0 0 0 -74 0 0 0 0 0 0 0 -75 0 0 0 0 0 0 0 -76 0 0 0 0 0 0 0 -77 0 0 0 0 0 0 0 -78 0 0 0 0 0 0 0 -79 0 0 0 0 0 0 0 -80 0 0 0 0 0 0 0 -81 0 0 0 0 0 0 0 -82 0 0 0 0 0 0 0 -83 0 0 0 0 0 0 0 -84 0 0 0 0 0 0 0 -85 0 0 0 0 0 0 0 -86 0 0 0 0 0 0 0 -87 0 0 0 0 0 0 0 -88 0 0 0 0 0 0 0 -89 0 0 0 0 0 0 0 -90 0 0 0 0 0 0 0 -91 0 0 0 0 0 0 0 -92 0 0 0 0 0 0 0 -93 0 0 0 0 0 0 0 -94 0 0 0 0 0 0 0 -95 0 0 0 0 0 0 0 -96 0 0 0 0 0 0 0 -97 0 0 0 0 0 0 0 -98 0 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 -100 0 0 0 0 0 0 0 -101 0 0 0 0 0 0 0 -102 0 0 0 0 0 0 0 -103 0 0 0 0 0 0 0 -104 0 0 0 0 0 0 0 -105 0 0 0 0 0 0 0 -106 0 0 0 0 0 0 0 -107 0 0 0 0 0 0 0 -108 0 0 0 0 0 0 0 -109 0 0 0 0 0 0 0 -110 0 0 0 0 0 0 0 -111 0 0 0 0 0 0 0 -112 0 0 0 0 0 0 0 -113 0 0 0 0 0 0 0 -114 0 0 0 0 0 0 0 -115 0 0 0 0 0 0 0 -116 0 0 0 0 0 0 0 -117 0 0 0 0 0 0 0 -118 0 0 0 0 0 0 0 -119 0 0 0 0 0 0 0 -120 0 0 0 0 0 0 0 -121 0 0 0 0 0 0 0 -122 0 0 0 0 0 0 0 -123 0 0 0 0 0 0 0 -124 0 0 0 0 0 0 0 -125 0 0 0 0 0 0 0 -126 0 0 0 0 0 0 0 -127 0 0 0 0 0 0 0 -128 0 0 0 0 0 0 0 -129 0 0 0 0 0 0 0 -130 0 0 0 0 0 0 0 -131 0 0 0 0 0 0 0 -132 0 0 0 0 0 0 0 -133 0 0 0 0 0 0 0 -134 0 0 0 0 0 0 0 -135 0 0 0 0 0 0 0 -136 0 0 0 0 0 0 0 -137 0 0 0 0 0 0 0 -138 0 0 0 0 0 0 0 -139 0 0 0 0 0 0 0 -140 0 0 0 0 0 0 0 -141 0 0 0 0 0 0 0 -142 0 0 0 0 0 0 0 -143 0 0 0 0 0 0 0 -144 0 0 0 0 0 0 0 -145 0 0 0 0 0 0 0 -146 0 0 0 0 0 0 0 -147 0 0 0 0 0 0 0 -148 0 0 0 0 0 0 0 -149 0 0 0 0 0 0 0 -150 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1638235704 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2898275634 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1902493234 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4016683054 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1638235704 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2898275634 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1902493234 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 1 1 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "100", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4016683054 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 100 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 11384421 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 11384421 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of interleaved paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 36753401 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/interleaved/output/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 32142888 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2714819290 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3802049955 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 99 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 1 0 1 -100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "99", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3867243128 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 99 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 99 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 1 0 1 -100 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "90", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,133 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4291984462 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 90 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 1 1 -89 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "90", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACNNNNNNNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTAC -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4294353461 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 90 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 1 1 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "90", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAANNNNNNNNNNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAA -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:98 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1485681 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 90 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 1 1 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 242897042 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 200 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGNNNNNNNNNNNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCNNNNNNN -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<: diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGC -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,137 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 236123159 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 178 -Average length of retained reads: 89 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 1 0 0 0 1 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACC -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGAT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*& diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 727785539 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 198 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/info.json adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/info.json --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities", "--minquality", "31"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATTCCGGCCTCATATTGGAAGCTACACGCTAGACCA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCTTCCAATATGAGGCCGGAATAACAAGCGTCGATG -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B@?@>>?@@=>><=;:9:9:9866852220.*&! diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TATCGAGCAACTCACCAAGTTCCTTTGATCCGAGGAACTACCCTTACGCCCATCGACGCTTGTTATT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -CATCTGGATTGTCGATCGCTGCCACCACTAGCCGGGTTTTTCTTTTGTAGTGGTCTAGCGTGTAGCT -+ -JHJIIJHJHIJJJGIGJGHHIGIIIHFFFIFGDFEFFFFEEEDCEDECBECCEDCAABBBBA@AA@B diff -Nru adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/excl_adapter/overlapping/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,111 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 737094053 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 31: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 2 -Number of retained nucleotides: 134 -Average length of retained reads: 67 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/your_output.collapsed adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/your_output.collapsed --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/your_output.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_AAGGGCSeq_1_5180_50 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,96 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 429139444 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/your_output.collapsed.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50 meta data -CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/collapse_truncated/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 505768950 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 1 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,96 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 429139444 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50/1 meta data -CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 505768950 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 1 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@M_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ -@M_AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,96 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 429139444 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 0 0 0 -50 0 0 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--trimns", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50/1 meta data -CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCT -+ -JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ&JJJJJJ -@MT_AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 505768950 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 1 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 -2 0 0 0 0 0 0 0 -3 0 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 -5 0 0 0 0 0 0 0 -6 0 0 0 0 0 0 0 -7 0 0 0 0 0 0 0 -8 0 0 0 0 0 0 0 -9 0 0 0 0 0 0 0 -10 0 0 0 0 0 0 0 -11 0 0 0 0 0 0 0 -12 0 0 0 0 0 0 0 -13 0 0 0 0 0 0 0 -14 0 0 0 0 0 0 0 -15 0 0 0 0 0 0 0 -16 0 0 0 0 0 0 0 -17 0 0 0 0 0 0 0 -18 0 0 0 0 0 0 0 -19 0 0 0 0 0 0 0 -20 0 0 0 0 0 0 0 -21 0 0 0 0 0 0 0 -22 0 0 0 0 0 0 0 -23 0 0 0 0 0 0 0 -24 0 0 0 0 0 0 0 -25 0 0 0 0 0 0 0 -26 0 0 0 0 0 0 0 -27 0 0 0 0 0 0 0 -28 0 0 0 0 0 0 0 -29 0 0 0 0 0 0 0 -30 0 0 0 0 0 0 0 -31 0 0 0 0 0 0 0 -32 0 0 0 0 0 0 0 -33 0 0 0 0 0 0 0 -34 0 0 0 0 0 0 0 -35 0 0 0 0 0 0 0 -36 0 0 0 0 0 0 0 -37 0 0 0 0 0 0 0 -38 0 0 0 0 0 0 0 -39 0 0 0 0 0 0 0 -40 0 0 0 0 0 0 0 -41 0 0 0 0 0 0 0 -42 0 0 0 0 0 0 0 -43 0 0 0 0 0 0 0 -44 0 0 0 0 0 0 0 -45 0 0 0 0 0 0 0 -46 0 0 0 0 0 0 0 -47 0 0 0 0 0 0 0 -48 0 0 0 0 0 0 0 -49 0 0 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC -@AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3738807510 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -N -+ -! -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3854997780 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50", "--interleaved-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.paired.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -N -+ -! -@AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/interleaved/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3934188119 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3738807510 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3854997780 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--trimns", "--minlength", "50"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/combined_output/keep_neither/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/combined_output/keep_neither/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3934188119 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "49"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1200660835 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 49 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "49", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1359054103 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 49 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 1 0 1 -50 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "49", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1361295368 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 49 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 1 0 1 -50 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/maxlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/both/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/both/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1436203328 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -NCATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -CATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -JJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1647601792 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 1 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate1/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "50", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -NGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.discarded adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.discarded --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -GGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -IHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1757553206 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 50 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 1 1 -50 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/minlength/mate2/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD -@read_150_10/1 -TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT -+ -<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2a.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2a.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_1/2 -AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC -+ -HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>E6,735@GG -@read_150_3/2 -GTCATTAACATTCACGAAGATAAATTTCTCCATTTTAAACAGAGACACTCAGTGAGCAGTAACCTGATTTTTTTTGGAATTTCATTCTTCAGGAGGGCTT -+ -HHHHHHHHHHHHHHHHHH?GF5:@AFHHHGHFDDGGFFFHHFGHHHGGHHHHHHHHFGHFGEGC.18984>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2b.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2b.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/2 -TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA -+ -HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 -@read_150_7/2 -ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT -+ -HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2c.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2c.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/input_2c.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/input_2c.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@read_150_9/2 -GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT -+ -GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= -@read_150_10/2 -TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA -+ -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,40 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD -@read_150_10/1 -TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT -+ -<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,40 +0,0 @@ -@read_150_1/2 -AGAAACCACAGTGACTTAAACAGAGAAAGTTTAATATAAATTTTTTAAAATTATGTTAAAAGAGCAATTATAATATATAAGTTAACTCTATGTGGTACCC -+ -HHHFFHHHHHHGFBGHHEFBDG?B=GHHFGFHFHHHHHHHFBFHHHHHGGEEG=DGGGGCHHHHHHHGEA%5ADHHHH=G&&*>>1BC=GFFAC<>E?..59&&-81:<<5.@ABCDBCE>:>@CDGHHHGEBFE/38@EEFBFGHHHHHHEGH?DHHHH>'9DEC**'*6 -@read_150_5/2 -TGGGGCCATCAGGAATTTTGCAGTGGTAATGGGGGACATTTTAGCTGAGACTTGGAAAAATGGTAGAATTTGCTCCAACATGAGGAAATATGAGCATTGA -+ -HHHHGEGHHHHGEG;/FHHHHHHHHE;@==G=DC>DGFHHHHHHHHHHHHHHFD;>A5<(@<4 -@read_150_7/2 -ACTTGCACCTCTTCATCAGAGGAGCAGATCCAGGAACAGAAGTCCTGCATTTACAGGCTCTTCATATCTTGTGCCGGGTTTGGCTGCCAGGTGGCCAGCT -+ -HHHHG=BDEDFFGGHHHHHHHHHHHHFHHFHHHCGHHHHHEBHHHHHHHHHHHHHHGEEE??6BCFHE624@7=1AFGBDHHHFFE<<.>,1349EEHHHHHHHGFHFHHHHHEHHD=:>-7@BC2BHHHHHHHGBHEFFHHGGHFGFHHEEFHFBEBEFHHFFBCA?B -@read_150_9/2 -GCCTTCCCTCTTCACTCCCTCCCTTATCCCAAACCTGCCTAGGTGGGGCTGATACAGACAGCAGGCCTGGCTCTACTTGTTTTGACAAAATATATGCCCT -+ -GGGEBGHHHHHHHHHHHHHHHHHHHHFADHHHFHHHF?DEF@B>C;CDGEHGGHHHE@@DBFGHHHHGB>BBFEGEGHFHF8ADCFDEE4D?>H@:>DD= -@read_150_10/2 -TAGTCTTCTCTTTCCTGAGAATATTTTTATTGCAAATATGTAGTCATATATACGTAAGATAAGGATATTTTAAATACTACTTTAAAAGTTATTACTATAA -+ -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHFFFGHHHHHHHHHHHHEBDG>CCBB?FHFHHDEFHGDDGHHHHHH@BECHHEHGDHHHHHFHHHGEHHHHH diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,144 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4274826581 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 10 -Number of unaligned read pairs: 4 -Number of well aligned read pairs: 6 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 20 -Number of retained nucleotides: 1970 -Average length of retained reads: 98.5 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 1 1 0 0 2 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 9 9 0 0 18 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 372265332 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/excl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2986012581 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAG -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBE diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimns/incl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3028896355 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 93 -Average length of retained reads: 46.5 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 1 0 0 1 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/default/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3078066396 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 100 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/info.json adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/info.json --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities", "--minquality", "35"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/input_1.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/input_1.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/input_2.fastq adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/input_2.fastq --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)! diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDE diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/2 data meta -AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATG -+ -JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDE diff -Nru adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.settings adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.settings --- adapterremoval-2.2.2/validation/pe/incl_adapter/trimqualities/minq35/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/incl_adapter/trimqualities/minq35/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3153498613 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 35: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 97 -Average length of retained reads: 48.5 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 1 0 0 0 1 -49 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/collapse/info.json adapterremoval-2.2.3/validation/pe/only_adapter/collapse/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/collapse/your_output.discarded adapterremoval-2.2.3/validation/pe/only_adapter/collapse/your_output.discarded --- adapterremoval-2.2.2/validation/pe/only_adapter/collapse/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/collapse/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_CTTTGTSeq_1_14286_0 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 416750178 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_CTTTGTSeq_1_14286_0/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_CTTTGTSeq_1_14286_0/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 416750178 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/info.json adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -N -+ -! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/combined_output/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/combined_output/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,44 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 688407609 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/info.json adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/your_output.discarded adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/your_output.discarded --- adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - -@CTTTGTSeq_1_14286_0/2 data meta - -+ - diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,44 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 861004460 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/defaults/info.json adapterremoval-2.2.3/validation/pe/only_adapter/defaults/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/defaults/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/defaults/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/defaults/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/defaults/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/defaults/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/defaults/your_output.discarded adapterremoval-2.2.3/validation/pe/only_adapter/defaults/your_output.discarded --- adapterremoval-2.2.2/validation/pe/only_adapter/defaults/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/defaults/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,8 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - -@CTTTGTSeq_1_14286_0/2 data meta - -+ - diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/defaults/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,44 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 861004460 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 2 2 diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/info.json adapterremoval-2.2.3/validation/pe/only_adapter/minlength/info.json --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "0"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/input_1.fastq adapterremoval-2.2.3/validation/pe/only_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/input_2.fastq adapterremoval-2.2.3/validation/pe/only_adapter/minlength/input_2.fastq --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta -AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -+ -JJJJJJHJIHHHHJJHIHJIGHIJHHIGHFHDFFGFFFGEDDFCDEDDEDCCCEDDBBB@CCAABA@@>@?>>?=?>=<;;<:99:7974554410-*'" diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.pair1.truncated adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.pair1.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.pair1.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.pair1.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.pair2.truncated adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.pair2.truncated --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.pair2.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.pair2.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/2 data meta - -+ - diff -Nru adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.settings adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/validation/pe/only_adapter/minlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/pe/only_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,44 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 934075502 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 0 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of discarded mate 2 reads: 0 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 2 -Number of retained reads: 2 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 1 1 0 0 2 diff -Nru adapterremoval-2.2.2/validation/README adapterremoval-2.2.3/validation/README --- adapterremoval-2.2.2/validation/README 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/README 1970-01-01 00:00:00.000000000 +0000 @@ -1,60 +0,0 @@ -Sequences: - No adapter - Short adapter - Long adapter - Complete adapter - -Filetypes: - Unix - Windows (\r\n) - - -Automatic variants? - - gzip - - bzip - - uncompressed - - -Single end: -x --collapse -x --combined-output -x --trimns -x --trimqualities -x --minlength -x --maxlength - - Bad: - --interleaved - --interleaved-input - --interleaved-output - - - - - - - - - -Possibilities: - - adapter - - overlap - - collapse (yes, no, yes but too short) - - lq trimming - - - -TODO: - - Single-end - - No adapter - - No adapter, lq trimming - - - - Single-end - - No adapter - - No adapter, lq trimming - - No adapter, overlapping - - No adapter, overlapping, lq trimming - - No adapter, overlapping, too short - - No adapter, overlapping, too short, lq trimming - diff -Nru adapterremoval-2.2.2/validation/run adapterremoval-2.2.3/validation/run --- adapterremoval-2.2.2/validation/run 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/run 1970-01-01 00:00:00.000000000 +0000 @@ -1,510 +0,0 @@ -#!/usr/bin/python -# -*- coding: utf-8 -*- -# Copyright (c) 2016 Mikkel Schubert -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -# SOFTWARE. -from __future__ import print_function - -import argparse -import bz2 -import cStringIO -import difflib -import gzip -import json -import os -import re -import subprocess -import sys -import tempfile -import types - - -############################################################################# -_COLORS_ENABLED = True - - -def _do_print_color(*vargs, **kwargs): - """Utility function: Prints using shell colors.""" - colorcode = kwargs.pop("colorcode") - destination = kwargs.pop("file", sys.stdout) - - # No colors if output is redirected (e.g. less, file, etc.) - if _COLORS_ENABLED and destination.isatty(): - vargs = list(vargs) - for (index, varg) in enumerate(vargs): - varg_lines = [] - # Newlines terminate the color-code for e.g. 'less', so ensure that - # each line is color-coded, while preserving the list of arguments - for line in str(varg).split("\n"): - varg_lines.append("\033[00;%im%s\033[00m" % (colorcode, line)) - vargs[index] = "\n".join(varg_lines) - - print(*vargs, file=destination, **kwargs) - - if '\n' in kwargs.get('end', '\n'): - destination.flush() - - -def print_ok(*vargs, **kwargs): - """Equivalent to print, but prints using shell colorcodes (green).""" - _do_print_color(*vargs, colorcode=32, **kwargs) - - -def print_err(*vargs, **kwargs): - """Equivalent to print, but prints using shell colorcodes (red).""" - _do_print_color(*vargs, colorcode=31, **kwargs) - - -############################################################################# -UNCOMPRESSED, GZIP, BZIP2 = "raw", "gz", "bz2" - - -def compress(value, compression): - fileobj = cStringIO.StringIO() - - if compression == GZIP: - handle = gzip.GzipFile('', 'w', 9, fileobj) - handle.write(value) - handle.close() - - return fileobj.getvalue() - elif compression == BZIP2: - return bz2.compress(value) - else: - assert False, compression - - -def decompress(filename): - with open(filename) as handle: - value = handle.read() - - if value and filename.endswith(".bz2"): - if not value.startswith("BZ"): - raise TestError("Expected bz2 file at %r, but header is %r" - % (filename, value[:2])) - - value = bz2.decompress(value) - elif value and filename.endswith(".gz"): - if not value.startswith("\x1f\x8b"): - raise TestError("Expected gzip file at %r, but header is %r" - % (filename, value[:2])) - - fileobj = cStringIO.StringIO(value) - handle = gzip.GzipFile('', 'r', 9, fileobj) - - value = handle.read() - - return cStringIO.StringIO(value).readlines() - - -############################################################################# -_EXEC = './build/AdapterRemoval' -_INFO_FILE = "info.json" -_INFO_FIELDS = { - 'arguments': types.ListType, - 'return_code': types.IntType, - 'stderr': types.ListType, -} - - -def pretty_output(s, padding=0, max_lines=float("inf")): - padding = " " * padding - lines = s.split("\n") - if len(lines) > max_lines: - lines = lines[:max_lines] - lines.append("...") - - result = [] - for line in lines: - result.append("%s> %s" % (padding, line)) - - return "\n".join(result) - - -def interleave(texts_1, texts_2): - files = [] - - for text_1, text_2 in zip(texts_1, texts_2): - lines_1 = text_1.split("\n") - lines_2 = text_2.split("\n") - iters = (iter(lines_1).next, iter(lines_2).next) - - assert len(lines_1) == len(lines_2) - - result = [] - while True: - try: - for it in iters: - for _ in xrange(4): - result.append(it()) - except StopIteration: - break - - files.append("\n".join(result)) - - return files - - -class TestError(StandardError): - pass - - -class TestCase(object): - def __init__(self, root, path): - self.root = root - self.path = path - self.name = " :: ".join(path) - self._files = self._collect_files(root) - self._info = self._read_info(os.path.join(root, _INFO_FILE)) - - def __repr__(self): - return "TestCase(%r)" % ({'root': self.root, - 'name': self.name, - 'info': self._info, - 'files': self._files}) - - def run(self, root): - root = os.path.join(root, *self.path) - - interleaved_tests = [False] - if self._is_properly_paired(): - interleaved_tests.append(True) - - for in_compression in (UNCOMPRESSED, GZIP, BZIP2): - for out_compression in (UNCOMPRESSED, GZIP, BZIP2): - for interleaved in interleaved_tests: - yield "%s>%s%s" % (in_compression, - out_compression, - ",intl" if interleaved else "") - - postfix = "%s_%s%s" % (in_compression, - out_compression, - "_intl" if interleaved else "") - - self._do_run(os.path.join(root, postfix), - in_compression, out_compression, interleaved) - - def _do_run(self, root, in_compression=UNCOMPRESSED, - out_compression=UNCOMPRESSED, interleaved=False): - assert in_compression in (UNCOMPRESSED, BZIP2, GZIP) - assert out_compression in (UNCOMPRESSED, BZIP2, GZIP) - os.makedirs(root) - - input_1, input_2 = self._setup_input(root, in_compression, interleaved) - self._do_call(root, input_1, input_2, out_compression, interleaved) - - self._check_file_creation(root, input_1, input_2, out_compression) - self._check_file_contents(root, out_compression) - - def _setup_input(self, root, compression, interleaved): - input_files = {} - for key in ("input_1", "input_2"): - input_files[key] = [open(filename).read() - for filename in self._files[key]] - - if interleaved: - input_files = {"input_1": interleave(input_files["input_1"], - input_files["input_2"]), - "input_2": []} - - final_files = {} - for key, values in input_files.iteritems(): - filenames = [] - for idx, value in enumerate(values): - filename = '%s%s.fastq' % (key, chr(ord('a') + idx)) - if compression != UNCOMPRESSED: - filename += "." + compression - value = compress(value, compression) - - with open(os.path.join(root, filename), "w") as handle: - handle.write(value) - - filenames.append(filename) - - final_files[key] = filenames - - if 'barcodes' in self._files: - with open(os.path.join(root, 'barcodes.txt'), 'w') as handle: - handle.writelines(self._files['barcodes']) - - return final_files["input_1"], final_files["input_2"] - - def _do_call(self, root, input_1, input_2, compression, interleaved): - command = self._build_command(root, input_1, input_2, - compression, interleaved) - - with open(os.devnull, "w") as dev_null: - proc = subprocess.Popen(command, - stdin=dev_null, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - close_fds=True, - preexec_fn=os.setsid, - cwd=root) - - stdout, stderr = proc.communicate() - if stdout: - raise TestError("Unexpected output to STDOUT: %r" % (stdout,)) - - for value in self._info["stderr"]: - if re.search(value, stderr) is None: - raise TestError("Expected value not found in output:\n" - " Searching for:\n%s\n STDERR:\n%s" - % (pretty_output(value, 4), - pretty_output(stderr, 4, 5))) - - if proc.returncode != self._info["return_code"]: - raise TestError("ERROR: Expected return-code %i, but " - "AdapterRemoval returned %i:\n%s" - % (self._info["return_code"], - proc.returncode, - pretty_output(stderr, 2, 5))) - - def _check_file_creation(self, root, input_1, input_2, compression): - expected_files = set(self._files["output"]) - if 'barcodes' in self._files: - expected_files.add('barcodes.txt') - - if compression != UNCOMPRESSED: - expected_files_ = set() - for value in expected_files: - if not value.endswith(".settings") and value != 'barcodes.txt': - expected_files_.add(value + "." + compression) - else: - expected_files_.add(value) - expected_files = expected_files_ - - observed_files = frozenset(os.listdir(root)) \ - - frozenset(input_1) - frozenset(input_2) - - if expected_files - observed_files: - raise TestError("ERROR: Expected output file(s) not created:\n" - " Expected: %r\n Observed: %r" - % (sorted(expected_files), sorted(observed_files))) - elif observed_files - expected_files: - raise TestError("ERROR: Unexpected output file(s) created: %r" - % (sorted(observed_files - expected_files))) - - def _check_file_contents(self, root, compression): - for filename, exp_data in sorted(self._files["output"].iteritems()): - obs_filename = os.path.join(root, filename) - if compression != UNCOMPRESSED: - if not filename.endswith(".settings"): - obs_filename += "." + compression - - exp_data = exp_data - obs_data = decompress(obs_filename) - - if filename.endswith(".settings"): - exp_data = self._mangle_settings(exp_data) - obs_data = self._mangle_settings(obs_data) - - self._diff_file_pair_contents(os.path.join(self.root, filename), - os.path.join(root, filename), - exp_data, obs_data) - - def _diff_file_pair_contents(self, exp_filename, obs_filename, exp_data, obs_data): - if exp_data != obs_data: - lines = "".join(difflib.unified_diff(exp_data, obs_data, - "expected", "observed")) - - raise TestError("ERROR: Output file(s) differ:\n" - " Expected: %r\n Observed: %r\n Diff:\n%s" - % (exp_filename, obs_filename, - pretty_output(lines, 4))) - - def _build_command(self, root, input_1, input_2, compression, interleaved): - command = [os.path.abspath(_EXEC)] - if interleaved: - command.append("--interleaved-input") - - if 'barcodes' in self._files: - command.extend(('--barcode-list', 'barcodes.txt')) - - if input_1 or input_2: - if compression == BZIP2: - command.append("--bzip2") - elif compression == GZIP: - command.append("--gzip") - - if input_1: - command.append('--file1') - command.extend(input_1) - if input_2: - command.append('--file2') - command.extend(input_2) - - command.extend(self._info['arguments']) - - return [field % {"ROOT": root} for field in command] - - def _is_properly_paired(self): - input_1 = self._files["input_1"] - input_2 = self._files["input_2"] - - return input_1 and len(input_1) == len(input_2) - - @classmethod - def _mangle_settings(cls, handle): - result = [] - for line in handle: - line = re.sub(r"RNG seed: [0-9]+", "RNG seed: NA", line) - line = re.sub(r"AdapterRemoval ver. [0-9]+.[0-9]+.[0-9]+[a-zA-Z]?", - "AdapterRemoval ver. X.Y.Z", line) - # Removed keyword to allow automatic interleaved tests - line = re.sub(r" interleaved paired-end reads", - r" paired-end reads", - line) - - result.append(line) - - return result - - @classmethod - def _collect_files(cls, root): - result = { - "input_1": [], - "input_2": [], - "output": {}, - } - - def read_lines(root, filename): - return open(os.path.join(root, filename)).readlines() - - abs_root = os.path.abspath(root) - for filename in sorted(os.listdir(root)): - if filename.startswith("input_1"): - result["input_1"].append(os.path.join(abs_root, filename)) - elif filename.startswith("input_2"): - result["input_2"].append(os.path.join(abs_root, filename)) - elif filename not in ('info.json', 'README', 'barcodes.txt'): - result["output"][filename] = read_lines(root, filename) - elif filename == 'barcodes.txt': - result["barcodes"] = read_lines(root, filename) - - return result - - @classmethod - def _read_info(cls, filename): - with open(filename) as handle: - text = handle.read() - raw_info = json.loads(text) - - if not isinstance(raw_info, types.DictType): - raise TestError('\'info.json\' does not contain dictionary.') - elif set(raw_info) - set(_INFO_FIELDS): - raise TestError('\'info.json\' does contains unexpected fields; ' - 'expected keys %r, but found keys unknown keys %r.' - % (sorted(_INFO_FIELDS), - sorted(set(raw_info) - set(_INFO_FIELDS)))) - - info = {"arguments": [], - "return_code": 0, - "stderr": []} - info.update(raw_info) - - for key, expected_type in _INFO_FIELDS.items(): - if not isinstance(info[key], expected_type): - raise TestError('Type of %r in \'info.json\' is %s, not a %s.' - % (key, type(info[key]), expected_type)) - elif isinstance(info[key], types.ListType): - for value in info[key]: - if not isinstance(value, types.StringTypes): - raise TestError('Type of value in %r in \'info.json\' ' - 'is %s, not a string.' - % (key, type(value))) - - return info - - @classmethod - def collect(cls, root, path=()): - tests = [] - - for filename in sorted(os.listdir(root)): - filepath = os.path.join(root, filename) - - if os.path.isdir(filepath): - tests.extend(cls.collect(filepath, path + (filename,))) - elif filename == 'info.json': - try: - test = TestCase(root, path) - except StandardError, error: - print_err("ERROR: %s reading test %r: %s" - % (error.__class__.__name__, - ' :: '.join(path), error)) - continue - - tests.append(test) - - return tests - - -def parse_args(argv): - parser = argparse.ArgumentParser() - parser.add_argument('work_dir', - help="Directory in which to run test-cases.") - parser.add_argument('source_dir', - help="Directory containing test-cases.") - - return parser.parse_args(argv) - - -def main(argv): - args = parse_args(argv) - if not os.path.exists(_EXEC): - print_err("ERROR: Executable does not exist: %r" % (_EXEC,)) - return 1 - - print('Reading test-cases from %r' % (args.source_dir,)) - tests = TestCase.collect(args.source_dir) - - if not os.path.exists(args.work_dir): - os.makedirs(args.work_dir) - - args.work_dir = tempfile.mkdtemp(dir=args.work_dir) - print('Writing test-cases results to %r' % (args.work_dir,)) - - n_failures = 0 - print('\nRunning tests:') - for idx, test in enumerate(tests, start=1): - print(" %i of %i: %s " % (idx, len(tests), test.name), end='') - label = 'unknown' - - try: - for label in test.run(args.work_dir): - print_ok(".", end="") - sys.stdout.flush() - except TestError, error: - n_failures += 1 - message = "\n ".join(str(error).split("\n")) - print_err(" %s for %s:\n %s" % (error.__class__.__name__, - label, message)) - else: - print_ok(" [OK]") - - if n_failures: - print_err("\n%i of %i tests failed .." % (n_failures, len(tests))) - else: - print_ok("\nAll %i tests succeeded .." % (len(tests),)) - - return n_failures - - -if __name__ == '__main__': - sys.exit(main(sys.argv[1:])) diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/collapse/info.json adapterremoval-2.2.3/validation/se/excl_adapter/collapse/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/collapse/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4051235691 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/collapse/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/collapse/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/collapse/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,145 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4051235691 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 0 0 0 0 -51 0 0 0 0 0 -52 0 0 0 0 0 -53 0 0 0 0 0 -54 0 0 0 0 0 -55 0 0 0 0 0 -56 0 0 0 0 0 -57 0 0 0 0 0 -58 0 0 0 0 0 -59 0 0 0 0 0 -60 0 0 0 0 0 -61 0 0 0 0 0 -62 0 0 0 0 0 -63 0 0 0 0 0 -64 0 0 0 0 0 -65 0 0 0 0 0 -66 0 0 0 0 0 -67 0 0 0 0 0 -68 0 0 0 0 0 -69 0 0 0 0 0 -70 0 0 0 0 0 -71 0 0 0 0 0 -72 0 0 0 0 0 -73 0 0 0 0 0 -74 0 0 0 0 0 -75 0 0 0 0 0 -76 0 0 0 0 0 -77 0 0 0 0 0 -78 0 0 0 0 0 -79 0 0 0 0 0 -80 0 0 0 0 0 -81 0 0 0 0 0 -82 0 0 0 0 0 -83 0 0 0 0 0 -84 0 0 0 0 0 -85 0 0 0 0 0 -86 0 0 0 0 0 -87 0 0 0 0 0 -88 0 0 0 0 0 -89 0 0 0 0 0 -90 0 0 0 0 0 -91 0 0 0 0 0 -92 0 0 0 0 0 -93 0 0 0 0 0 -94 0 0 0 0 0 -95 0 0 0 0 0 -96 0 0 0 0 0 -97 0 0 0 0 0 -98 0 0 0 0 0 -99 0 0 0 0 0 -100 1 0 0 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/collapse/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "999"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 999 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/discarded/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/info.json adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/combined_output/retained/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/crlf_newlines/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/crlf_newlines/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/defaults/info.json adapterremoval-2.2.3/validation/se/excl_adapter/defaults/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/defaults/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/defaults/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/defaults/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/defaults/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/defaults/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/info.json adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "13"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/your_output.discarded adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/your_output.discarded --- adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/maxlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/maxlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1833120783 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 13 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/minlength/info.json adapterremoval-2.2.3/validation/se/excl_adapter/minlength/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/minlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "999"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/minlength/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/minlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/minlength/your_output.discarded adapterremoval-2.2.3/validation/se/excl_adapter/minlength/your_output.discarded --- adapterremoval-2.2.2/validation/se/excl_adapter/minlength/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/minlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/minlength/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/minlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1752967089 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 999 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 217798732 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 100 -Average length of retained reads: 100 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 0 0 0 -100 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/excl_ns/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/excl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAANNNNNN -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,137 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 87921694 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 94 -Average length of retained reads: 94 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/trimns/incl_ns/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimns/incl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGNTCAACGATTAAA -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:977775532 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,142 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1434085985 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 99 -Average length of retained reads: 99 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 0 0 0 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/default/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/default/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)' diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/info.json adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/info.json --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities", "--minquality", "31"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/input_1.fastq adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/input_1.fastq --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTG -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A@@@?>>@==<=<;;;;<:9777755321/,)'! diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/your_output.settings adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/your_output.settings --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,110 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1585058107 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 31: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 67 -Average length of retained reads: 67 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/your_output.truncated adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/your_output.truncated --- adapterremoval-2.2.2/validation/se/excl_adapter/trimqualities/minq31/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/excl_adapter/trimqualities/minq31/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTAT -+ -JJIJIIJIIIJJGJHGGHJJJFGHGIJHEGHFGGGFFFFFFEEEDDGDCDBECDCACBC@@CBAA@A diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse/info.json adapterremoval-2.2.3/validation/se/incl_adapter/collapse/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse/your_output.collapsed adapterremoval-2.2.3/validation/se/incl_adapter/collapse/your_output.collapsed --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse/your_output.collapsed 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse/your_output.collapsed 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 566778642 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/info.json adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/your_output.collapsed.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/collapse_truncated/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 566778642 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 1 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/info.json adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,95 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1432823771 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of full-length collapsed pairs: 1 -Number of truncated collapsed pairs: 0 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 0 0 0 -50 0 1 0 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/info.json adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--collapse", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCNAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,94 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1432823771 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 1 -Number of retained reads: 1 -Number of retained nucleotides: 49 -Average length of retained reads: 49 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 0 0 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 0 0 0 -31 0 0 0 0 0 -32 0 0 0 0 0 -33 0 0 0 0 0 -34 0 0 0 0 0 -35 0 0 0 0 0 -36 0 0 0 0 0 -37 0 0 0 0 0 -38 0 0 0 0 0 -39 0 0 0 0 0 -40 0 0 0 0 0 -41 0 0 0 0 0 -42 0 0 0 0 0 -43 0 0 0 0 0 -44 0 0 0 0 0 -45 0 0 0 0 0 -46 0 0 0 0 0 -47 0 0 0 0 0 -48 0 0 0 0 0 -49 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/collapse_truncated/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@MT_AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDEC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "999"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1529034138 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 999 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/discarded/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -N -+ -! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/info.json adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 1756794576 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/combined_output/retained/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/info.json adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 667770639 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/crlf_newlines/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/crlf_newlines/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/defaults/info.json adapterremoval-2.2.3/validation/se/incl_adapter/defaults/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/defaults/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/defaults/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 667770639 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/defaults/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/defaults/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/defaults/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/defaults/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/info.json adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--maxlength", "13"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/your_output.discarded adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/your_output.discarded --- adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/maxlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/maxlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2394757988 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 13 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/minlength/info.json adapterremoval-2.2.3/validation/se/incl_adapter/minlength/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/minlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "999"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/minlength/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/minlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/minlength/your_output.discarded adapterremoval-2.2.3/validation/se/incl_adapter/minlength/your_output.discarded --- adapterremoval-2.2.2/validation/se/incl_adapter/minlength/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/minlength/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/minlength/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/minlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2314668317 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 999 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/info.json adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/input_1a.fastq adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/input_1a.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/input_1a.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/input_1a.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGAAGATCGGAAGAGCAC -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59/''.CCFHFHHHHHH -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACAA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHHF diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/input_1b.fastq adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/input_1b.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/input_1b.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/input_1b.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD -@read_150_10/1 -TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT -+ -<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,143 +0,0 @@ -AdapterRemoval ver. 2.2.0 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 35713051 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 10 -Number of unaligned reads: 8 -Number of well aligned reads: 2 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 10 -Number of reads with adapters[1]: 2 -Number of retained reads: 10 -Number of retained nucleotides: 984 -Average length of retained reads: 98.4 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 0 0 0 -51 0 0 0 -52 0 0 0 -53 0 0 0 -54 0 0 0 -55 0 0 0 -56 0 0 0 -57 0 0 0 -58 0 0 0 -59 0 0 0 -60 0 0 0 -61 0 0 0 -62 0 0 0 -63 0 0 0 -64 0 0 0 -65 0 0 0 -66 0 0 0 -67 0 0 0 -68 0 0 0 -69 0 0 0 -70 0 0 0 -71 0 0 0 -72 0 0 0 -73 0 0 0 -74 0 0 0 -75 0 0 0 -76 0 0 0 -77 0 0 0 -78 0 0 0 -79 0 0 0 -80 0 0 0 -81 0 0 0 -82 0 0 0 -83 0 0 0 -84 0 0 0 -85 1 0 1 -86 0 0 0 -87 0 0 0 -88 0 0 0 -89 0 0 0 -90 0 0 0 -91 0 0 0 -92 0 0 0 -93 0 0 0 -94 0 0 0 -95 0 0 0 -96 0 0 0 -97 0 0 0 -98 0 0 0 -99 1 0 1 -100 8 0 8 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/multiple_input/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/multiple_input/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,40 +0,0 @@ -@read_150_1/1 -CTTGGGTACTCAGCCTTAGGGTACCACATAGAGTTATCTTATATATTATAATTGCTCTTTTAACATAATTTTAAAAAATTTATATTAAACTTTCTCTGTT -+ -HHHFFFFBBDGGGGGHHHHHGGFCDHGEE<@;+@C792A.CEEGGFFFFDEFGFHHHH@C2;@F;EDDHFDCCC@.DEEEG=BGEDC5>:=2@GFHHHFF -@read_150_2/1 -GAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAAAGA -+ -HHHHHHHHHHHHHHHHHHHHHHHGC.@CFGHHHHHHHHFBFFHEHHHHFBGHFFFFFFHEDE@EBHHFHB<<>099BEB@=?*59 -@read_150_3/1 -TATGTAATGACATAACTCTTATGGGCAACTTCACAAAAACACAGAAGAAAGCCCTCCTAAAGAATGAAATTCCAAAAAAAATCAGGTTACTGCTCACTGA -+ -HHE=EE@DBBBGHGBFGGDDDDFFFHHHHHGHHHHHHGHHHE7BFHHHHHHG@4FEHHFHHHHFHHHHHHFFFE?EGCDE>CD:9=>+*;=37::ADDHF -@read_150_4/1 -CTCCTATATAAAGATAGCTCTGTAAAACAGGCCAAAAAGCAGAGTGGGGTGTGGGAAGGCAGGGAAAACTGTCCAGGAATAAAGGCATGAAATGAAACA -+ -HHHHHHHHHHHHHHHHEG@:EEB4DFHHEHFHHHHEGFFEEFCDHEFF:+1;?GFFCFHHHHHHHHHFHBB>>BEDGCDHHHH -@read_150_5/1 -TACTCACGGACAAAGAATAAATATAGCTCCTCCAGGAGCTTAATAACTCAGTGCTGTCTAAACTCCTTACACCTGATGTTGATGCCATGGTTAGATAGTT -+ -HHFFGGFDBHHEHHHHHHHHHHHHFHHHHFHHFEEDFD8=GHFFHHDHHHCHHFDHBHD:> -@read_150_7/1 -TAAGTAAGGTAGACAGCTAAGTCTAGTTTGTTCCCAGTGTTGTACCAGTCTCATCAGTGCCGTGTCTGGGTCTCACAGCCTCTGGTGTTCTATGCTGGAT -+ -GFFEEDHHGHHHHHHHHB?GG77-/:>>@?6AC5GIB?BEBHHHHHHHHHHHHFGFHHHHHHEFEGF9?EHHHE@8BB12BEHHH -@read_150_8/1 -TAAAAACAAAAACCCTGATGAGAGTATTGATGTGTGCATAAACAAAGAAAAACATAATAGGAATAGAATGGTGAATTAAATTTTGTGAATTTTGGAAACC -+ -HGGGGGHHHHHFHHGHHHHHHHEHHHHHHFHHEEHHHHHFE:/CGBHHHHHGFFGHHHHCEHEFECEFHHFEEE>CFFFCE?DEBD -@read_150_10/1 -TATAGATGAACTCTGATTTAGAATTTGTATAAGCTAAAGCATTATAGTAATAACTTTTAAAGTAGTATTTAAAATATCCTTATCTTACGTATATATGACT -+ -<506@6?GHHHHGFHGFCFHHHHHHHHHHFGFF<3@C43F>AAEEFBFDFFHHHHHHHHED(0DAEBEFC?BFBEHHHHHC@85@GBGGFDCHEHHFCFB diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/info.json adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "1"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 667770639 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/one/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/one/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/info.json adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "3"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 667770639 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/three/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/three/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/info.json adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--threads", "2"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 667770639 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/threads/two/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/threads/two/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/info.json adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2489899758 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/excl_ns/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/excl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/info.json adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCNNNNNNNNATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,87 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2566824554 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 44 -Average length of retained reads: 44 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/trimns/incl_ns/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimns/incl_ns/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGC -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFF diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/info.json adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,93 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2679028121 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 50 -Average length of retained reads: 50 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 0 0 0 -46 0 0 0 -47 0 0 0 -48 0 0 0 -49 0 0 0 -50 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/default/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/default/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/info.json adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/info.json --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimqualities", "--minquality", "36"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/input_1.fastq adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/input_1.fastq --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)! diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/your_output.settings adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/your_output.settings --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,88 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 2816594278 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 36: Yes -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 45 -Average length of retained reads: 45 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 0 0 0 -31 0 0 0 -32 0 0 0 -33 0 0 0 -34 0 0 0 -35 0 0 0 -36 0 0 0 -37 0 0 0 -38 0 0 0 -39 0 0 0 -40 0 0 0 -41 0 0 0 -42 0 0 0 -43 0 0 0 -44 0 0 0 -45 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/your_output.truncated adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/your_output.truncated --- adapterremoval-2.2.2/validation/se/incl_adapter/trimqualities/minq36/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/incl_adapter/trimqualities/minq36/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@AAGGGCSeq_1_5180_50/1 meta data -ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCA -+ -IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFF diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/collapse/info.json adapterremoval-2.2.3/validation/se/only_adapter/collapse/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/collapse/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/collapse/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--collapse"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/collapse/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/collapse/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/collapse/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/collapse/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/collapse/your_output.discarded adapterremoval-2.2.3/validation/se/only_adapter/collapse/your_output.discarded --- adapterremoval-2.2.2/validation/se/only_adapter/collapse/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/collapse/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@M_CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/collapse/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/collapse/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/collapse/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/collapse/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,45 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4215296776 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: Yes -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of full-length collapsed pairs: 0 -Number of truncated collapsed pairs: 0 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Collapsed CollapsedTruncated Discarded All -0 0 0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/info.json adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 913821732 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/your_output.truncated adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/your_output.truncated --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/discarded/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/discarded/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -N -+ -! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/info.json adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--combined-output", "--minlength", "0"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 984265443 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 0 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/your_output.truncated adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/your_output.truncated --- adapterremoval-2.2.2/validation/se/only_adapter/combined_output/retained/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/combined_output/retained/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/info.json adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/your_output.discarded adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/your_output.discarded --- adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/crlf_newlines/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/crlf_newlines/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4288002672 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/defaults/info.json adapterremoval-2.2.3/validation/se/only_adapter/defaults/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/defaults/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/defaults/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": [], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/defaults/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/defaults/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/defaults/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/defaults/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/defaults/your_output.discarded adapterremoval-2.2.3/validation/se/only_adapter/defaults/your_output.discarded --- adapterremoval-2.2.2/validation/se/only_adapter/defaults/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/defaults/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/defaults/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/defaults/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/defaults/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/defaults/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 4288002672 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 1 -Number of singleton mate 1 reads: 0 -Number of reads with adapters[1]: 1 -Number of retained reads: 0 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 0 1 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/minlength/info.json adapterremoval-2.2.3/validation/se/only_adapter/minlength/info.json --- adapterremoval-2.2.2/validation/se/only_adapter/minlength/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/minlength/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--minlength", "0"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/minlength/input_1.fastq adapterremoval-2.2.3/validation/se/only_adapter/minlength/input_1.fastq --- adapterremoval-2.2.2/validation/se/only_adapter/minlength/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/minlength/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data -AGATCGGAAGAGCACACGTCTGAACTCCATTCACCTTTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -+ -JGIJJJIJIJJGJGJIHHHGGIGIHGHGGGHEHEGFDFGEEEEGCFDDCCECDCBBCBBACCAA@BACB?>>>>?;=<;=<<::;:9777664010.-)! diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/minlength/your_output.settings adapterremoval-2.2.3/validation/se/only_adapter/minlength/your_output.settings --- adapterremoval-2.2.2/validation/se/only_adapter/minlength/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/minlength/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,43 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 120751608 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 2: No -Trimming using sliding windows: No -Minimum genomic length: 0 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 0 -Number of well aligned reads: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 1 -Number of retained reads: 1 -Number of retained nucleotides: 0 -Average length of retained reads: 0 - - -[Length distribution] -Length Mate1 Discarded All -0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/se/only_adapter/minlength/your_output.truncated adapterremoval-2.2.3/validation/se/only_adapter/minlength/your_output.truncated --- adapterremoval-2.2.2/validation/se/only_adapter/minlength/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/se/only_adapter/minlength/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@CTTTGTSeq_1_14286_0/1 meta data - -+ - diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/info.json adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/info.json --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimwindows", "4", "--minquality", "20"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/input_1.fastq adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/input_1.fastq --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT -+ -7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/input_2.fastq adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/input_2.fastq --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTA -+ -IGHHFEIIIGFC5675565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.discarded adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.discarded --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGG -+ -IGHHFEIIIGFC diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.settings adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.settings --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,74 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 20: Yes -Trimming using sliding windows: 4 -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 30 -Average length of retained reads: 30 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 1 1 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 0 0 0 -28 0 0 0 0 0 -29 0 0 0 0 0 -30 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.singleton.truncated adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/trimwindows/pe/excl_n/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/excl_n/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -NNTCAACAATAGGGTTTACGACCTCGATGN -+ -IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/info.json adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/info.json --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/input_1.fastq adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/input_1.fastq --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT -+ -7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/input_2.fastq adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/input_2.fastq --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/input_2.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/input_2.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGGTTGTAGTA -+ -IGHHFEIIIGFC5675565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.discarded adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.discarded --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.discarded 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.discarded 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/2 data meta -GTCAGCGAAGGG -+ -IGHHFEIIIGFC diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.settings adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.settings --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,71 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of paired-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 981230521 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 20: Yes -Trimming using sliding windows: 4 -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 - - -[Trimming statistics] -Total number of read pairs: 1 -Number of unaligned read pairs: 0 -Number of well aligned read pairs: 1 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of discarded mate 2 reads: 1 -Number of singleton mate 2 reads: 0 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 27 -Average length of retained reads: 27 - - -[Length distribution] -Length Mate1 Mate2 Singleton Discarded All -0 0 0 0 0 0 -1 0 0 0 0 0 -2 0 0 0 0 0 -3 0 0 0 0 0 -4 0 0 0 0 0 -5 0 0 0 0 0 -6 0 0 0 0 0 -7 0 0 0 0 0 -8 0 0 0 0 0 -9 0 0 0 0 0 -10 0 0 0 0 0 -11 0 0 0 0 0 -12 0 0 0 1 1 -13 0 0 0 0 0 -14 0 0 0 0 0 -15 0 0 0 0 0 -16 0 0 0 0 0 -17 0 0 0 0 0 -18 0 0 0 0 0 -19 0 0 0 0 0 -20 0 0 0 0 0 -21 0 0 0 0 0 -22 0 0 0 0 0 -23 0 0 0 0 0 -24 0 0 0 0 0 -25 0 0 0 0 0 -26 0 0 0 0 0 -27 0 0 1 0 1 diff -Nru adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.singleton.truncated adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.singleton.truncated --- adapterremoval-2.2.2/validation/trimwindows/pe/incl_n/your_output.singleton.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/pe/incl_n/your_output.singleton.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCAACAATAGGGTTTACGACCTCGATG -+ -IIIJJGJHGJJJGHJJJFGIIIGFC?: diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/excl_n/info.json adapterremoval-2.2.3/validation/trimwindows/se/excl_n/info.json --- adapterremoval-2.2.2/validation/trimwindows/se/excl_n/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/excl_n/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimwindows", "4", "--minquality", "20"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/excl_n/input_1.fastq adapterremoval-2.2.3/validation/trimwindows/se/excl_n/input_1.fastq --- adapterremoval-2.2.2/validation/trimwindows/se/excl_n/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/excl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT -+ -7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/excl_n/your_output.settings adapterremoval-2.2.3/validation/trimwindows/se/excl_n/your_output.settings --- adapterremoval-2.2.2/validation/trimwindows/se/excl_n/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/excl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,73 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: No -Trimming Phred scores <= 20: Yes -Trimming using sliding windows: 4 -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 30 -Average length of retained reads: 30 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 0 0 0 -28 0 0 0 -29 0 0 0 -30 1 0 1 diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/excl_n/your_output.truncated adapterremoval-2.2.3/validation/trimwindows/se/excl_n/your_output.truncated --- adapterremoval-2.2.2/validation/trimwindows/se/excl_n/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/excl_n/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -NNTCAACAATAGGGTTTACGACCTCGATGN -+ -IIIIIJJGJHGJJJGHJJJFGIIIGFC?:7 diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/incl_n/info.json adapterremoval-2.2.3/validation/trimwindows/se/incl_n/info.json --- adapterremoval-2.2.2/validation/trimwindows/se/incl_n/info.json 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/incl_n/info.json 1970-01-01 00:00:00.000000000 +0000 @@ -1,6 +0,0 @@ -{ - "arguments": ["--trimwindows", "4", "--minquality", "20", "--trimns"], - "return_code": 0, - "stderr": [ - ] -} diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/incl_n/input_1.fastq adapterremoval-2.2.3/validation/trimwindows/se/incl_n/input_1.fastq --- adapterremoval-2.2.2/validation/trimwindows/se/incl_n/input_1.fastq 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/incl_n/input_1.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCCANNTCAACAATAGGGTTTACGACCTCGATGNTGGAT -+ -7555IIIIIJJGJHGJJJGHJJJFGIIIGFC?:75565+ diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/incl_n/your_output.settings adapterremoval-2.2.3/validation/trimwindows/se/incl_n/your_output.settings --- adapterremoval-2.2.2/validation/trimwindows/se/incl_n/your_output.settings 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/incl_n/your_output.settings 1970-01-01 00:00:00.000000000 +0000 @@ -1,70 +0,0 @@ -AdapterRemoval ver. 2.1.7 -Trimming of single-end reads - - -[Adapter sequences] -Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT - - -[Adapter trimming] -RNG seed: 3702281079 -Alignment shift value: 2 -Global mismatch threshold: 0.333333 -Quality format (input): Phred+33 -Quality score max (input): 41 -Quality format (output): Phred+33 -Quality score max (output): 41 -Mate-number separator (input): '/' -Trimming Ns: Yes -Trimming Phred scores <= 20: Yes -Trimming using sliding windows: 4 -Minimum genomic length: 15 -Maximum genomic length: 4294967295 -Collapse overlapping reads: No -Minimum overlap (in case of collapse): 11 -Minimum adapter overlap: 0 - - -[Trimming statistics] -Total number of reads: 1 -Number of unaligned reads: 1 -Number of well aligned reads: 0 -Number of discarded mate 1 reads: 0 -Number of singleton mate 1 reads: 1 -Number of reads with adapters[1]: 0 -Number of retained reads: 1 -Number of retained nucleotides: 27 -Average length of retained reads: 27 - - -[Length distribution] -Length Mate1 Discarded All -0 0 0 0 -1 0 0 0 -2 0 0 0 -3 0 0 0 -4 0 0 0 -5 0 0 0 -6 0 0 0 -7 0 0 0 -8 0 0 0 -9 0 0 0 -10 0 0 0 -11 0 0 0 -12 0 0 0 -13 0 0 0 -14 0 0 0 -15 0 0 0 -16 0 0 0 -17 0 0 0 -18 0 0 0 -19 0 0 0 -20 0 0 0 -21 0 0 0 -22 0 0 0 -23 0 0 0 -24 0 0 0 -25 0 0 0 -26 0 0 0 -27 1 0 1 diff -Nru adapterremoval-2.2.2/validation/trimwindows/se/incl_n/your_output.truncated adapterremoval-2.2.3/validation/trimwindows/se/incl_n/your_output.truncated --- adapterremoval-2.2.2/validation/trimwindows/se/incl_n/your_output.truncated 2017-07-17 14:08:34.000000000 +0000 +++ adapterremoval-2.2.3/validation/trimwindows/se/incl_n/your_output.truncated 1970-01-01 00:00:00.000000000 +0000 @@ -1,4 +0,0 @@ -@ATAGCCSeq_1_2959_500/1 meta data -TCAACAATAGGGTTTACGACCTCGATG -+ -IIIJJGJHGJJJGHJJJFGIIIGFC?: