diff -Nru blasr-5.3.3+dfsg/debian/changelog blasr-5.3.3+dfsg/debian/changelog --- blasr-5.3.3+dfsg/debian/changelog 2020-05-28 15:44:06.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/changelog 2020-11-16 12:51:01.000000000 +0000 @@ -1,26 +1,13 @@ -blasr (5.3.3+dfsg-4build4) groovy; urgency=medium +blasr (5.3.3+dfsg-5) unstable; urgency=medium - * No-change rebuild against libpbbam1.0.7 + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Repository, Repository-Browse. + * Versioned Build-Depends: libblasr-dev (>= 5.3.4+dfsg-3~) since other + Debian releases put header file on wrong location - -- Steve Langasek Thu, 28 May 2020 15:44:06 +0000 - -blasr (5.3.3+dfsg-4build3) groovy; urgency=medium - - * No-change rebuild against libpbcopper1.6.0 - - -- Steve Langasek Wed, 27 May 2020 01:13:58 +0000 - -blasr (5.3.3+dfsg-4build2) groovy; urgency=medium - - * No-change rebuild against libhdf5-103-1 - - -- Graham Inggs Wed, 13 May 2020 17:45:38 +0000 - -blasr (5.3.3+dfsg-4build1) focal; urgency=medium - - * No-change rebuild for libgcc-s1 package name change. - - -- Matthias Klose Mon, 23 Mar 2020 07:10:47 +0100 + -- Andreas Tille Mon, 16 Nov 2020 13:51:01 +0100 blasr (5.3.3+dfsg-4) unstable; urgency=medium diff -Nru blasr-5.3.3+dfsg/debian/control blasr-5.3.3+dfsg/debian/control --- blasr-5.3.3+dfsg/debian/control 2020-05-27 01:13:58.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/control 2020-11-16 12:51:01.000000000 +0000 @@ -1,10 +1,9 @@ Source: blasr -Maintainer: Ubuntu Developers -XSBC-Original-Maintainer: Debian Med Packaging Team +Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), python3, meson, cmake, @@ -17,11 +16,12 @@ libpbdata-dev, libpbcopper-dev, libgtest-dev, - libblasr-dev (>= 5.3.3+dfsg-2) + libblasr-dev (>= 5.3.4+dfsg-3~) Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Homepage: https://github.com/PacificBiosciences/blasr +Rules-Requires-Root: no Package: blasr Architecture: any diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/loadPulses.1 blasr-5.3.3+dfsg/debian/old_manpages/loadPulses.1 --- blasr-5.3.3+dfsg/debian/old_manpages/loadPulses.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/loadPulses.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,73 +0,0 @@ -.TH LOADPULSES "1" "July 2015" "loadPulses 3ca7fe8" "User Commands" -.SH NAME -loadPulses \- load sequencing pulse information -.SH SYNOPSIS -.B loadPulses -.I basFileName -.I cmpFileName -.RI [ options ] -.SH DESCRIPTION -.B loadPulses -loads sequencing pulse information such as inter-pulse distance or quality -information into the cmp.h5 file. -This allows one to analyze kinetic and quality information by alignment column. -.SH OPTIONS -.TP -.I basFileName -The input {bas,pls}.h5 or input.fofn. -.TP -.I cmpFileName -The cmp.h5 file to load pulse information into. -.TP -.BI \-metrics \0value -A comma separated list of metrics (with no spaces). -.RS -.TP -Valid options are: -WhenStarted, QualityValue, InsertionQV, MergeQV, -DeletionQV, DeletionTag, SubstitutionTag, SubstitutionQV, PreBaseFrames, IPD, -StartFrame, PulseWidth, WidthInFrames, Light, pkmid, ClassifierQV, PulseIndex -.TP -Default options are: -QualityValue, ClassifierQV, StartFrame, PulseWidth, -WidthInFrames, pkmid, IPD -.RE -.TP -.B \-failOnMissingData -Exit if any data fields are missing from the bas.h5 or pls.h5 -input that are required to load a metric. Defualt is a warning. -.TP -.B \-byread -Load pulse information by read rather than buffering metrics. -.TP -.B \-bymetric -Load pulse information by metric rather than by read. This uses -more memory than \fB\-byread\fR, but can be faster. -.TP -.BI \-maxElements \0value -Set a limit on the size of pls/bas file to buffer in with -\fB\-bymetric\fR (default value: maximum int). Use \fB\-byread\fR if the limit -is exceeded. -.TP -.BI \-maxMemory \0value -Set a limit (in GB) on the memory to buffer data with \fB\-bymetric\fR -(default value: 4 GB). Use \fB\-byread\fR if the limit is exceeded. -.TP -.BI \-metaNElements \0value -Set number of elements in meta data cache for reading -bas/bax/pls.h5 file. -.TP -.BI \-rawNElements value -Set number of elements in raw data cache for reading the bas/bax/pls.h5 file. -.TP -.BI \-rawChunkSize \0value -Set chunk size of raw data cache for reading the bas/bax/pls.h5 file. -.SH SEE ALSO -.BR blasr (1) -.BR pls2fasta (1) -.BR samFilter (1) -.BR samtoh5 (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR sdpMatcher (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/pls2fasta.1 blasr-5.3.3+dfsg/debian/old_manpages/pls2fasta.1 --- blasr-5.3.3+dfsg/debian/old_manpages/pls2fasta.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/pls2fasta.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,69 +0,0 @@ -.TH PLS2FASTA "1" "July 2015" "pls2fasta 3ca7fe8" "User Commands" -.SH NAME -pls2fasta \- convert plx.h5/bax.h5/fofn files to fasta or fastq files -.SH SYNOPSIS -.B pls2fasta -.I in.bax.h5 -.I out.fasta -.RI [ options ] -.SH DESCRIPTION -Although fasta files are provided with every run, they are not trimmed nor -split into subreads. This program takes additional annotation -information, such as the subread coordinates and high quality regions, -and uses them to create fasta sequences that are substrings of all -bases called. Most of the time, you will want to trim low quality -reads, so you should specify \fB\-trimByRegion\fR. -.SH OPTIONS -.TP -.I in.bax.h5 -Input plx.h5/bax.h5/fofn file. -.TP -.I out.fasta -Output fasta/fastq file. -.TP -.B \-trimByRegion -Trim away low quality regions. -.TP -.B \-maskByRegion -Mask low quality regions with 'N'. -.TP -.BI \-regionTable \0value -Optional HDF file with a \fI\,/PulseData/Regions\/\fP dataset. -.TP -.BI \-minSubreadLength \0value -Do not write subreads less than the specified length. -.TP -.B \-noSplitSubreads -Do not split reads on adapter sequences. -.TP -.B \-holeNumber -Only print this hole number (or list of numbers). -.TP -.B \-fastq -Print in FASTQ format with quality. -.TP -.B \-ccs -Print de novo circular consensus (ccs) sequences -.TP -.B \-lineLength \0value -Specify fasta/fastq line length -.TP -.BI \-minReadScore \0value -Minimum read score to print a read. -The score is a number between 0 and 1000 and represents the expected accuracy -percentage * 10. A typical value would be between 750 and 800. -This does not apply to ccs reads. -.TP -.B \-best -If a ccs sequence exists, print this. -Otherwise, print the longest subread. -This does not support fastq. -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR samFilter (1) -.BR samtoh5 (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR sdpMatcher (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/samFilter.1 blasr-5.3.3+dfsg/debian/old_manpages/samFilter.1 --- blasr-5.3.3+dfsg/debian/old_manpages/samFilter.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/samFilter.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,134 +0,0 @@ -.TH SAMFILTER "1" "July 2015" "samFilter 3ca7fe8" "User Commands" -.SH NAME -samFilter \- filter nucleotide sequence alignments in SAM files -.SH SYNOPSIS -.B samFilter -.I file.sam -.I reference.fasta -.I out.sam -.RI [ options ] -.SH OPTIONS -.TP -.I file.sam -Input SAM file. -.TP -.I reference.fasta -Reference used to generate reads. -.TP -.I out.sam -Output SAM file. -.TP -.BI \-minAlnLength \0value -(50) Report alignments only if their lengths are greater than -\fIvalue\fR. -.TP -.BI \-minAlignLength \0value -Alias of \fB\-minAlnLength\fR -.TP -.BI \-minLength \0value -Alias of \fB\-minAlnLength\fR -.TP -.BI \-minPctSimilarity \0value -.IP -(70) Report alignments only if their percentage similairty is -greater than \fIvalue\0. -.TP -.BI \-minPctIdentity \0value -Alias of \fB\-minPctSimilarity\fR -.TP -.BI \-minPctAccuracy \0value -(70) Report alignments only if their percentage accuray is -greater than \fIvalue\fR. -.TP -.BI \-minAccuracy \0value -Alias of \fB\-minPctAccuracy\fR -.TP -.BI \-hitPolicy \0value -(randombest) Specify a policy to treat multiple hits from [all, -allbest, random, randombest, leftmost] -.RS -.TP -.I all -report all alignments. -.TP -.I allbest -report all equally top scoring alignments. -.TP -.I random -report a random alignment. -.TP -.I randombest -report a random alignment from multiple equally top scoring alignments. -.TP -.I leftmost -report an alignment which has the best alignmentscore and has the smallest -mapping coordinate in any reference. -.RE -.TP -.BI \-scoreSign \0value -(\-1) Whether higher or lower scores are better. -.RS -.TP -\-1 -lower is better -.TP -1 -higher is better. -.RE -.TP -.BI \-scoreCutoff \0value -(INF) Report alignments only if their scores are no worse than -\fIvalue\fR. -.TP -.BI \-seed \0value -(1) Seed for random number generator. -If seed is 0, then use current time as seed. -.TP -.BI \-holeNumbers \0value -A string of comma-delimited hole number ranges to output hits, -such as '1,2,10-12'. This requires hit titles to be in SMRT read -title format. -.TP -.B \-smrtTitle -Use this option when filtering alignments generated by programs -other than -.BR blasr (1), -e.g. bwa\-sw or gmap. Parse read coordinates -from the SMRT read title. The title is in the format -\fI\,/name/hole/coordinates\/\fP, where coordinates are in the format -\ed+_\ed+, and represent the interval of the read that was -aligned. -.TP -.BI \-titleTable \0value -Use this experimental option when filtering alignments generated -by -.BR blasr (1) -with \fB\-titleTable\fR titleTableName, in which case -reference titles in SAM are represented by their indices (e.g., -0, 1, 2, ...) in the title table. -.TP -.BI \-filterAdapterOnly \0value -Use this option to remove reads which can only map to adapters -specified in the GFF file. -.TP -.B \-v -Be verbose. -.SH NOTES -Because SAM has optional tags that have different meanings in different -programs, careful usage is required in order to have proper output. The -"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM -.RB ( blasr (1)) -it is defined as the start in the query sequence of the alignment. -When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not -specified, the coordinates given by the xs and xe tags are used to define -the interval of a read that is aligned. The CIGAR string is relative to -this interval. -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR pls2fasta (1) -.BR samtoh5 (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR sdpMatcher (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/samtoh5.1 blasr-5.3.3+dfsg/debian/old_manpages/samtoh5.1 --- blasr-5.3.3+dfsg/debian/old_manpages/samtoh5.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/samtoh5.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,62 +0,0 @@ -.TH SAMTOH5 "1" "July 2015" "samtoh5 3ca7fe8" "User Commands" -.SH NAME -samtoh5 \- convert a SAM file to cmp.h5 format -.SH SYNOPSIS -.B samtoh5 -.I in.sam -.I reference.fasta -.I out.cmp.h5 -.RI [ options ] -.SH OPTIONS -.TP -.I in.sam -Input SAM file. -.TP -.I reference.fasta -Reference used to generate reads. -.TP -.I out.cmp.h5 -Output cmp.h5 file. -.TP -.B \-smrtTitle -Use this option when converting alignments generated from reads -produced by the -.BR pls2fasta (1) -from bas.h5 files by parsing read -coordinates from the SMRT read title. The title is in the -format \fI\,/name/hole/coordinates\/\fP, where coordinates are in the -format \ed+_\ed+, and represent the interval of the read that was -aligned. -.TP -.BI \-readType \0value -Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA' -.TP -.BI \-verbosity \0value -Set desired verbosity. -.TP -.B \-useShortRefName -Use abbreviated reference names obtained from \fIfile.sam\fR instead -of using full names from \fIreference.fasta\fR. -.TP -.B \-copyQVs -Copy all QVs available in the SAM file into the cmp.h5 file. -This includes things like InsertionQV and DeletionTag. -.SH NOTES -Because SAM has optional tags that have different meanings in different -programs, careful usage is required in order to have proper output. The -"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM -.RB ( blasr (1)) -it is defined as the start in the query sequence of the alignment. -When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not -specified, the coordinates given by the xs and xe tags are used to define -the interval of a read that is aligned. The CIGAR string is relative to -this interval. -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR pls2fasta (1) -.BR samFilter (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR sdpMatcher (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/samtom4.1 blasr-5.3.3+dfsg/debian/old_manpages/samtom4.1 --- blasr-5.3.3+dfsg/debian/old_manpages/samtom4.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/samtom4.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,39 +0,0 @@ -.TH SAMTOM4 "1" "July 2015" "samtom4 3ca7fe8" "User Commands" -.SH NAME -samtom4 \- Convert a SAM file generated by -.BR blasr (1) -to M4 format -.SH SYNOPSIS -.B samtom4 -.I in.sam -.I reference.fasta -.I out.m4 -.RI [ options ] -.SH OPTIONS -.TP -.I in.sam -Input SAM file, which is produced by blasr. -.TP -.I reference.fasta -Reference used to generate \fIfile.sam\fR. -.TP -.I out.m4 -Output in -.BR blasr (1) -M4 format. -.TP -.B \-header -Print M4 header. -.TP -.B \-useShortRefName -Use abbreviated reference names obtained from \fIfile.sam\fR instead -of using full names from \fIreference.fasta\fR. -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR pls2fasta (1) -.BR samFilter (1) -.BR samtoh5 (1) -.BR sawriter (1) -.BR sdpMatcher (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/sdpMatcher.1 blasr-5.3.3+dfsg/debian/old_manpages/sdpMatcher.1 --- blasr-5.3.3+dfsg/debian/old_manpages/sdpMatcher.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/sdpMatcher.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,33 +0,0 @@ -.TH SDPMATCHER "1" "July 2015" "sdpMatcher 3ca7fe8" "User Commands" -.SH NAME -sdpMatcher \- nucleotide sequence matching using sparse dynamic programming -.SH SYNOPSIS -.B sdpMatcher -.I query -.I target -.I k -.RB [ \-indelRate -.IR delta ] -.RB [ \-showalign ] -.RB [ \-printsw ] -.RB [ \-noRefine ] -.RB [ \-indel -.IR i ] -.RB [ \-local ] -.RB [ \-match -.IR m ] -.RB [ \-sdpIndel -.IR i ] -.SH DESCRIPTION -Performs sparse dynamic programming (SDP) between pairs of sequences as they -are given in two FASTA files, called \fIquery\fR and \fItarget\fR for -convenience. \fIk\fR is the size of the k-mer used for the SDP algorithm. -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR pls2fasta (1) -.BR samFilter (1) -.BR samtoh5 (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR toAfg (1) diff -Nru blasr-5.3.3+dfsg/debian/old_manpages/toAfg.1 blasr-5.3.3+dfsg/debian/old_manpages/toAfg.1 --- blasr-5.3.3+dfsg/debian/old_manpages/toAfg.1 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/old_manpages/toAfg.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,23 +0,0 @@ -.TH TOAFG "1" "July 2015" "toAfg 3ca7fe8" "User Commands" -.SH NAME -toAfg \- Print reads stored in a file (pls|fasta|fastq) as an afg. -.SH SYNOPSIS -.B toAfg -.I input.filetype \0output.filetype -.RB [ \-minSubreadLength -.IR l ] -.RB [ \-regionTable -.IR regions_file ] -.RB [ \-noSplitSubreads ] -.RB [ \-useccsdenovo ] -.RB [ \-uniformQV -.IR QV ] -.SH SEE ALSO -.BR blasr (1) -.BR loadPulses (1) -.BR pls2fasta (1) -.BR samFilter (1) -.BR samtoh5 (1) -.BR samtom4 (1) -.BR sawriter (1) -.BR sdpMatcher (1) diff -Nru blasr-5.3.3+dfsg/debian/salsa-ci.yml blasr-5.3.3+dfsg/debian/salsa-ci.yml --- blasr-5.3.3+dfsg/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/salsa-ci.yml 2020-11-16 12:51:01.000000000 +0000 @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff -Nru blasr-5.3.3+dfsg/debian/upstream/metadata blasr-5.3.3+dfsg/debian/upstream/metadata --- blasr-5.3.3+dfsg/debian/upstream/metadata 2020-01-22 16:48:33.000000000 +0000 +++ blasr-5.3.3+dfsg/debian/upstream/metadata 2020-11-16 12:51:01.000000000 +0000 @@ -19,3 +19,5 @@ Entry: Blasr - Name: conda:bioconda Entry: blasr +Repository: https://github.com/PacificBiosciences/blasr.git +Repository-Browse: https://github.com/PacificBiosciences/blasr