diff -Nru bio-tradis-1.4.1+dfsg/bcinstall.log bio-tradis-1.4.5+dfsg2/bcinstall.log --- bio-tradis-1.4.1+dfsg/bcinstall.log 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bcinstall.log 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,7 @@ +--> Working on Bio::Tradis +Fetching http://www.cpan.org/authors/id/S/SS/SSJUNNEBO/Bio-Tradis-1.4.1.tar.gz ... OK +Configuring Bio-Tradis-1.4.1 ... OK +==> Found dependencies: Moose +--> Working on Moose +Fetching http://www.cpan.org/authors/id/E/ET/ETHER/Moose-2.2011.tar.gz ... OK +Configuring Moose-2.2011 ... N/A diff -Nru bio-tradis-1.4.1+dfsg/bin/add_tradis_tags bio-tradis-1.4.5+dfsg2/bin/add_tradis_tags --- bio-tradis-1.4.1+dfsg/bin/add_tradis_tags 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/add_tradis_tags 2019-12-04 14:40:22.000000000 +0000 @@ -1,20 +1,50 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::DetectTags; +$Bio::Tradis::Bin::DetectTags::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: check if tr tag is present # PODNAME: check_tags -=head1 SYNOPSIS - -Checks the presence of tr/tq tags in a given BAM file - -=cut BEGIN { unshift( @INC, '../lib' ) } BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } use Bio::Tradis::CommandLine::AddTags; Bio::Tradis::CommandLine::AddTags->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +check_tags - check if tr tag is present + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Checks the presence of tr/tq tags in a given BAM file + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/bacteria_tradis bio-tradis-1.4.5+dfsg2/bin/bacteria_tradis --- bio-tradis-1.4.1+dfsg/bin/bacteria_tradis 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/bacteria_tradis 2019-12-04 14:40:22.000000000 +0000 @@ -1,21 +1,52 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::RunTradis; +$Bio::Tradis::Bin::RunTradis::VERSION = '1.4.5'; +use FindBin qw($Bin); + # ABSTRACT: Perform full tradis analysis # PODNAME: run_tradis + +BEGIN { unshift( @INC, '../lib' ) } +BEGIN { unshift( @INC, './lib' ) } +# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } + +use Bio::Tradis::CommandLine::TradisAnalysis; + +Bio::Tradis::CommandLine::TradisAnalysis->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +run_tradis - Perform full tradis analysis + +=head1 VERSION + +version 1.4.5 + =head1 SYNOPSIS Take a fastq, reference and a tag and generates insertion site plots for use in Artemis -=cut +=head1 AUTHOR -BEGIN { unshift( @INC, '../lib' ) } -BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +Carla Cummins -use Bio::Tradis::CommandLine::TradisAnalysis; +=head1 COPYRIGHT AND LICENSE -Bio::Tradis::CommandLine::TradisAnalysis->new(args => \@ARGV, script_name => $0)->run; +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/check_tradis_tags bio-tradis-1.4.5+dfsg2/bin/check_tradis_tags --- bio-tradis-1.4.1+dfsg/bin/check_tradis_tags 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/check_tradis_tags 2019-12-04 14:40:22.000000000 +0000 @@ -1,20 +1,50 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::DetectTags; +$Bio::Tradis::Bin::DetectTags::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: check if tr tag is present # PODNAME: check_tags -=head1 SYNOPSIS - -Checks the presence of tr/tq tags in a given BAM file - -=cut BEGIN { unshift( @INC, '../lib' ) } BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } use Bio::Tradis::CommandLine::CheckTags; Bio::Tradis::CommandLine::CheckTags->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +check_tags - check if tr tag is present + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Checks the presence of tr/tq tags in a given BAM file + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/combine_tradis_plots bio-tradis-1.4.5+dfsg2/bin/combine_tradis_plots --- bio-tradis-1.4.1+dfsg/bin/combine_tradis_plots 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/combine_tradis_plots 2019-12-04 14:40:22.000000000 +0000 @@ -1,23 +1,53 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::CombineTradisPlots; +$Bio::Tradis::Bin::CombineTradisPlots::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files # PODNAME: combine_tradis_plot + +BEGIN { unshift( @INC, '../lib' ) } +BEGIN { unshift( @INC, './lib' ) } +# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } + +use Bio::Tradis::CommandLine::PlotCombine; + +Bio::Tradis::CommandLine::PlotCombine->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +combine_tradis_plot - Combine multiple plotfiles and generate updated statistics for the combined files + +=head1 VERSION + +version 1.4.5 + =head1 SYNOPSIS Takes a tab-delimited file with an ID as the first column followed by a list of plotfiles to combine per row. The ID will be used to name the new plotfile and as an identifier in the stats file, so ensure these are unique. -=cut +=head1 AUTHOR -BEGIN { unshift( @INC, '../lib' ) } -BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +Carla Cummins -use Bio::Tradis::CommandLine::PlotCombine; +=head1 COPYRIGHT AND LICENSE -Bio::Tradis::CommandLine::PlotCombine->new(args => \@ARGV, script_name => $0)->run; +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/filter_tradis_tags bio-tradis-1.4.5+dfsg2/bin/filter_tradis_tags --- bio-tradis-1.4.1+dfsg/bin/filter_tradis_tags 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/filter_tradis_tags 2019-12-04 14:40:22.000000000 +0000 @@ -1,21 +1,51 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::FilterTags; +$Bio::Tradis::Bin::FilterTags::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: filter tags at start of fastq sequences # PODNAME: filter_tags + +BEGIN { unshift( @INC, '../lib' ) } +BEGIN { unshift( @INC, './lib' ) } +# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } + +use Bio::Tradis::CommandLine::FilterFastqTags; + +Bio::Tradis::CommandLine::FilterFastqTags->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +filter_tags - filter tags at start of fastq sequences + +=head1 VERSION + +version 1.4.5 + =head1 SYNOPSIS Checks tags at the start of the fastq sequence and returns a file containing those that match the tag provided -=cut +=head1 AUTHOR -BEGIN { unshift( @INC, '../lib' ) } -BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +Carla Cummins -use Bio::Tradis::CommandLine::FilterFastqTags; +=head1 COPYRIGHT AND LICENSE -Bio::Tradis::CommandLine::FilterFastqTags->new(args => \@ARGV, script_name => $0)->run; +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/remove_tradis_tags bio-tradis-1.4.5+dfsg2/bin/remove_tradis_tags --- bio-tradis-1.4.1+dfsg/bin/remove_tradis_tags 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/remove_tradis_tags 2019-12-04 14:40:22.000000000 +0000 @@ -1,20 +1,50 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::RemoveTags; +$Bio::Tradis::Bin::RemoveTags::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: remove user specified tags from start of fastq sequences # PODNAME: remove_tags -=head1 SYNOPSIS - -Removes tags from the sequence and quality strings based on user input - -=cut BEGIN { unshift( @INC, '../lib' ) } BEGIN { unshift( @INC, './lib' ) } BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } use Bio::Tradis::CommandLine::RemoveFastqTags; Bio::Tradis::CommandLine::RemoveFastqTags->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +remove_tags - remove user specified tags from start of fastq sequences + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Removes tags from the sequence and quality strings based on user input + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/tradis_comparison.R bio-tradis-1.4.5+dfsg2/bin/tradis_comparison.R --- bio-tradis-1.4.1+dfsg/bin/tradis_comparison.R 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/tradis_comparison.R 2019-12-04 14:40:22.000000000 +0000 @@ -3,7 +3,7 @@ # PODNAME: tradis_comparison.R # ABSTRACT: tradis_comparison.R -library("edgeR") +if(!require(edgeR)){install.packages("edgeR", repos = "http://cran.us.r-project.org")} library("getopt") options(width=80) diff -Nru bio-tradis-1.4.1+dfsg/bin/tradis_gene_insert_sites bio-tradis-1.4.5+dfsg2/bin/tradis_gene_insert_sites --- bio-tradis-1.4.1+dfsg/bin/tradis_gene_insert_sites 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/tradis_gene_insert_sites 2019-12-04 14:40:22.000000000 +0000 @@ -1,32 +1,13 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::GeneInsertSites; +$Bio::Tradis::Bin::GeneInsertSites::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: Generate insertion site details from TraDIS pipeline plots # PODNAME: tradis_gene_insert_sites -=head1 NAME - -tradis_gene_insert_sites.pl - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -This script is for TRADIS analysis. It takes in a plot file created by the TRADIS pathogen informatics pipeline, and an embl file of -annotation. -It then outputs a tab delimited file with the insert site details. This is then used as input to an R script to calculate essentialit -y. - -=head1 CONTACT - -path-help@sanger.ac.uk -Original author: Lars Barquist - -=head1 METHODS - -=cut use strict; use warnings; @@ -327,3 +308,51 @@ { ['locus_tag','gene_name','ncrna','start','end','strand','read_count','ins_index','gene_length','ins_count','fcn']; } + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +tradis_gene_insert_sites - Generate insertion site details from TraDIS pipeline plots + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +=head1 DESCRIPTION + +This script is for TRADIS analysis. It takes in a plot file created by the TRADIS pathogen informatics pipeline, and an embl file of +annotation. +It then outputs a tab delimited file with the insert site details. This is then used as input to an R script to calculate essentialit +y. + +=head1 NAME + +tradis_gene_insert_sites.pl + +=head1 CONTACT + +path-help@sanger.ac.uk +Original author: Lars Barquist + +=head1 METHODS + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/tradis_merge_plots bio-tradis-1.4.5+dfsg2/bin/tradis_merge_plots --- bio-tradis-1.4.1+dfsg/bin/tradis_merge_plots 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/tradis_merge_plots 2019-12-04 14:40:22.000000000 +0000 @@ -1,33 +1,16 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::MergePlots; +$Bio::Tradis::Bin::MergePlots::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: # PODNAME: tradis_merge_plots -=head1 NAME - -tradis_merge_plots - -=head1 SYNOPSIS - -tradis_merge_plots - Given a study name or ID, group by sample and tag, and generate tab files for input to R. - -=head1 DESCRIPTION - -Given a study name or ID, group by sample and tag, and generate tab files for input to R. - -=head1 CONTACT - -path-help@sanger.ac.uk - -=head1 METHODS - -=cut package TraDISMergePlots::Main; - +$TraDISMergePlots::Main::VERSION = '1.4.5'; use Moose; use Getopt::Long; use File::Basename; @@ -96,3 +79,49 @@ } } } + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +tradis_merge_plots - + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +tradis_merge_plots - Given a study name or ID, group by sample and tag, and generate tab files for input to R. + +=head1 DESCRIPTION + +Given a study name or ID, group by sample and tag, and generate tab files for input to R. + +=head1 NAME + +tradis_merge_plots + +=head1 CONTACT + +path-help@sanger.ac.uk + +=head1 METHODS + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/bin/tradis_plot bio-tradis-1.4.5+dfsg2/bin/tradis_plot --- bio-tradis-1.4.1+dfsg/bin/tradis_plot 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/bin/tradis_plot 2019-12-04 14:40:22.000000000 +0000 @@ -1,21 +1,51 @@ #!/usr/bin/env perl package Bio::Tradis::Bin::TradisPlot; +$Bio::Tradis::Bin::TradisPlot::VERSION = '1.4.5'; +use FindBin qw($Bin); # ABSTRACT: Generate plots as part of a tradis analysis # PODNAME: tradis_plot -=head1 SYNOPSIS - -Generate insertion plots for Artemis from a mapped fastq file and -a reference in GFF format - -=cut BEGIN { unshift( @INC, '../lib' ) } BEGIN { unshift( @INC, './lib' ) } BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) } +BEGIN { unshift( @INC, "$Bin/../lib/" ) } use Bio::Tradis::CommandLine::PlotTradis; Bio::Tradis::CommandLine::PlotTradis->new(args => \@ARGV, script_name => $0)->run; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +tradis_plot - Generate plots as part of a tradis analysis + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Generate insertion plots for Artemis from a mapped fastq file and +a reference in GFF format + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/build/bwa-0.7.17.tbz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/build/bwa-0.7.17.tbz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/build/samtools-1.3.tbz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/build/samtools-1.3.tbz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/build/smalt-0.7.6.tgz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/build/smalt-0.7.6.tgz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/build/tabix-master.tgz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/build/tabix-master.tgz differ diff -Nru bio-tradis-1.4.1+dfsg/CHANGELOG.md bio-tradis-1.4.5+dfsg2/CHANGELOG.md --- bio-tradis-1.4.1+dfsg/CHANGELOG.md 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/CHANGELOG.md 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,198 @@ +# Change Log + +## [Unreleased](https://github.com/sanger-pathogens/Bio-Tradis/tree/HEAD) + +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.4.1...HEAD) + +**Merged pull requests:** + +- Include tests in README [\#97](https://github.com/sanger-pathogens/Bio-Tradis/pull/97) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [v1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.4.1) (2018-09-20) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.1...v1.4.1) + +**Merged pull requests:** + +- update version for cpan [\#96](https://github.com/sanger-pathogens/Bio-Tradis/pull/96) ([ssjunnebo](https://github.com/ssjunnebo)) +- Add to codecov [\#95](https://github.com/sanger-pathogens/Bio-Tradis/pull/95) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.1) (2018-07-19) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.0...1.4.1) + +**Closed issues:** + +- Installation on Ubuntu 17.10 fails [\#84](https://github.com/sanger-pathogens/Bio-Tradis/issues/84) +- Port 18 volume discrepancy? [\#83](https://github.com/sanger-pathogens/Bio-Tradis/issues/83) + +**Merged pull requests:** + +- Change TryCatch to Try::Tiny [\#94](https://github.com/sanger-pathogens/Bio-Tradis/pull/94) ([ssjunnebo](https://github.com/ssjunnebo)) +- fix typo in badge [\#93](https://github.com/sanger-pathogens/Bio-Tradis/pull/93) ([ssjunnebo](https://github.com/ssjunnebo)) +- Include TOC [\#92](https://github.com/sanger-pathogens/Bio-Tradis/pull/92) ([ssjunnebo](https://github.com/ssjunnebo)) +- 621538 docker [\#91](https://github.com/sanger-pathogens/Bio-Tradis/pull/91) ([ssjunnebo](https://github.com/ssjunnebo)) +- 621538 docker [\#90](https://github.com/sanger-pathogens/Bio-Tradis/pull/90) ([ssjunnebo](https://github.com/ssjunnebo)) +- include reference genome for cram [\#89](https://github.com/sanger-pathogens/Bio-Tradis/pull/89) ([ssjunnebo](https://github.com/ssjunnebo)) +- Revert "Replace cram file without reads" [\#88](https://github.com/sanger-pathogens/Bio-Tradis/pull/88) ([ssjunnebo](https://github.com/ssjunnebo)) +- Replace cram file without reads [\#87](https://github.com/sanger-pathogens/Bio-Tradis/pull/87) ([ssjunnebo](https://github.com/ssjunnebo)) +- update tutorial for ENA switch to https \(from http\) [\#85](https://github.com/sanger-pathogens/Bio-Tradis/pull/85) ([lbarquist](https://github.com/lbarquist)) + +## [1.4.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.0) (2017-11-28) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.3...1.4.0) + +**Closed issues:** + +- Duplicate genes [\#81](https://github.com/sanger-pathogens/Bio-Tradis/issues/81) +- Installing Bio-Tradis Fail [\#80](https://github.com/sanger-pathogens/Bio-Tradis/issues/80) + +**Merged pull requests:** + +- include last base of annotation in insertion count [\#82](https://github.com/sanger-pathogens/Bio-Tradis/pull/82) ([lbarquist](https://github.com/lbarquist)) +- Rename license file' [\#79](https://github.com/sanger-pathogens/Bio-Tradis/pull/79) ([ssjunnebo](https://github.com/ssjunnebo)) +- update AUTHORS and rename LICENSE [\#78](https://github.com/sanger-pathogens/Bio-Tradis/pull/78) ([ssjunnebo](https://github.com/ssjunnebo)) +- Tmp file time stamp [\#77](https://github.com/sanger-pathogens/Bio-Tradis/pull/77) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [v1.3.3](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.3) (2017-05-08) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.2...v1.3.3) + +**Merged pull requests:** + +- try localtime for tmp file timestamp [\#76](https://github.com/sanger-pathogens/Bio-Tradis/pull/76) ([ssjunnebo](https://github.com/ssjunnebo)) + +## [v1.3.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.2) (2017-05-08) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.1...v1.3.2) + +**Closed issues:** + +- cpan update? [\#75](https://github.com/sanger-pathogens/Bio-Tradis/issues/75) +- tradis\_comparison.R error [\#71](https://github.com/sanger-pathogens/Bio-Tradis/issues/71) + +**Merged pull requests:** + +- modified ranges to accommodate higher density insertion data [\#74](https://github.com/sanger-pathogens/Bio-Tradis/pull/74) ([lbarquist](https://github.com/lbarquist)) +- removed File::Slurp [\#73](https://github.com/sanger-pathogens/Bio-Tradis/pull/73) ([vaofford](https://github.com/vaofford)) +- dont add POD to R scripts [\#72](https://github.com/sanger-pathogens/Bio-Tradis/pull/72) ([andrewjpage](https://github.com/andrewjpage)) + +## [v1.3.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.1) (2016-09-23) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.0...v1.3.1) + +**Closed issues:** + +- Mapping score always set to 1 if -m option used with plot\_tradis [\#66](https://github.com/sanger-pathogens/Bio-Tradis/issues/66) +- Error in step 3.5 of bacteria\_tradis, using samtools 1.3 [\#63](https://github.com/sanger-pathogens/Bio-Tradis/issues/63) + +**Merged pull requests:** + +- change to dist zilla starter bundle [\#70](https://github.com/sanger-pathogens/Bio-Tradis/pull/70) ([nds](https://github.com/nds)) +- switch PCR primers [\#69](https://github.com/sanger-pathogens/Bio-Tradis/pull/69) ([andrewjpage](https://github.com/andrewjpage)) +- updated readme [\#68](https://github.com/sanger-pathogens/Bio-Tradis/pull/68) ([lbarquist](https://github.com/lbarquist)) +- Fix for bug \#66, change mapping\_score option spec in B::T::CL::PlotTradis [\#67](https://github.com/sanger-pathogens/Bio-Tradis/pull/67) ([RoyChaudhuri](https://github.com/RoyChaudhuri)) + +## [v1.3.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.0) (2016-04-13) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.4...v1.3.0) + +**Merged pull requests:** + +- Merge Roys changes [\#65](https://github.com/sanger-pathogens/Bio-Tradis/pull/65) ([andrewjpage](https://github.com/andrewjpage)) +- added recipes \(again\) [\#62](https://github.com/sanger-pathogens/Bio-Tradis/pull/62) ([lbarquist](https://github.com/lbarquist)) + +## [v1.2.4](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.4) (2015-12-11) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.3...v1.2.4) + +**Closed issues:** + +- tradis\_essentiality.R [\#28](https://github.com/sanger-pathogens/Bio-Tradis/issues/28) + +**Merged pull requests:** + +- fixes for revision [\#61](https://github.com/sanger-pathogens/Bio-Tradis/pull/61) ([lbarquist](https://github.com/lbarquist)) +- bugfix to tradis\_essentiality.R [\#60](https://github.com/sanger-pathogens/Bio-Tradis/pull/60) ([lbarquist](https://github.com/lbarquist)) + +## [v1.2.3](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.3) (2015-11-03) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.2...v1.2.3) + +**Merged pull requests:** + +- Bump the version number [\#59](https://github.com/sanger-pathogens/Bio-Tradis/pull/59) ([bewt85](https://github.com/bewt85)) +- Ticket 463867: What if a tag isn't found? [\#58](https://github.com/sanger-pathogens/Bio-Tradis/pull/58) ([bewt85](https://github.com/bewt85)) +- updated bacteria\_tradis help messages [\#57](https://github.com/sanger-pathogens/Bio-Tradis/pull/57) ([lbarquist](https://github.com/lbarquist)) +- Add package version module to dist zilla [\#56](https://github.com/sanger-pathogens/Bio-Tradis/pull/56) ([andrewjpage](https://github.com/andrewjpage)) + +## [v1.2.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.2) (2015-09-14) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2.1...v1.2.2) + +**Merged pull requests:** + +- Added sequencing recipes [\#55](https://github.com/sanger-pathogens/Bio-Tradis/pull/55) ([lbarquist](https://github.com/lbarquist)) +- updated help messages for R scripts [\#54](https://github.com/sanger-pathogens/Bio-Tradis/pull/54) ([lbarquist](https://github.com/lbarquist)) +- POD formatting [\#53](https://github.com/sanger-pathogens/Bio-Tradis/pull/53) ([andrewjpage](https://github.com/andrewjpage)) + +## [v1.2.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2.1) (2015-09-10) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.2...v1.2.1) + +**Merged pull requests:** + +- Simplify installation [\#52](https://github.com/sanger-pathogens/Bio-Tradis/pull/52) ([andrewjpage](https://github.com/andrewjpage)) + +## [v1.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.2) (2015-09-08) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.132190...v1.2) + +**Merged pull requests:** + +- Ticket 473325: Install two different versions of SAMTOOLS [\#51](https://github.com/sanger-pathogens/Bio-Tradis/pull/51) ([bewt85](https://github.com/bewt85)) +- Add TravisCI support [\#50](https://github.com/sanger-pathogens/Bio-Tradis/pull/50) ([bewt85](https://github.com/bewt85)) +- fixed filtering bug [\#49](https://github.com/sanger-pathogens/Bio-Tradis/pull/49) ([lbarquist](https://github.com/lbarquist)) +- Updated shebang line in R scripts for portability [\#48](https://github.com/sanger-pathogens/Bio-Tradis/pull/48) ([carlacummins](https://github.com/carlacummins)) +- added installation notes [\#47](https://github.com/sanger-pathogens/Bio-Tradis/pull/47) ([lbarquist](https://github.com/lbarquist)) +- only require 2 command line args, not 3 [\#46](https://github.com/sanger-pathogens/Bio-Tradis/pull/46) ([lbarquist](https://github.com/lbarquist)) +- Bug fixes and added features [\#45](https://github.com/sanger-pathogens/Bio-Tradis/pull/45) ([carlacummins](https://github.com/carlacummins)) +- Adding tabix a prerequisite [\#44](https://github.com/sanger-pathogens/Bio-Tradis/pull/44) ([js21](https://github.com/js21)) +- Cram file output [\#43](https://github.com/sanger-pathogens/Bio-Tradis/pull/43) ([andrewjpage](https://github.com/andrewjpage)) +- Code is now cross-platform [\#42](https://github.com/sanger-pathogens/Bio-Tradis/pull/42) ([js21](https://github.com/js21)) +- Pass through samtools exec and verbose mode [\#41](https://github.com/sanger-pathogens/Bio-Tradis/pull/41) ([andrewjpage](https://github.com/andrewjpage)) +- Cram support [\#40](https://github.com/sanger-pathogens/Bio-Tradis/pull/40) ([andrewjpage](https://github.com/andrewjpage)) +- added the missing test files [\#39](https://github.com/sanger-pathogens/Bio-Tradis/pull/39) ([js21](https://github.com/js21)) +- suppressed uninitialised warnings when importing PE data [\#38](https://github.com/sanger-pathogens/Bio-Tradis/pull/38) ([carlacummins](https://github.com/carlacummins)) +- Tabix indexed plot files in place [\#37](https://github.com/sanger-pathogens/Bio-Tradis/pull/37) ([js21](https://github.com/js21)) +- added filtering option, so default is old behavior. -f now enables read ... [\#36](https://github.com/sanger-pathogens/Bio-Tradis/pull/36) ([lbarquist](https://github.com/lbarquist)) +- fixed typo [\#35](https://github.com/sanger-pathogens/Bio-Tradis/pull/35) ([lbarquist](https://github.com/lbarquist)) +- feature addition to tradis\_comparison, bugfix tradis\_essentiality [\#34](https://github.com/sanger-pathogens/Bio-Tradis/pull/34) ([lbarquist](https://github.com/lbarquist)) +- Added AUTHORS file [\#33](https://github.com/sanger-pathogens/Bio-Tradis/pull/33) ([aslett1](https://github.com/aslett1)) +- Fixed problem with opening combined plots in Artemis [\#32](https://github.com/sanger-pathogens/Bio-Tradis/pull/32) ([carlacummins](https://github.com/carlacummins)) +- Fixed problem with unusual characters in filenames [\#31](https://github.com/sanger-pathogens/Bio-Tradis/pull/31) ([carlacummins](https://github.com/carlacummins)) +- Updates [\#30](https://github.com/sanger-pathogens/Bio-Tradis/pull/30) ([carlacummins](https://github.com/carlacummins)) +- index needs to be offset by 2 [\#29](https://github.com/sanger-pathogens/Bio-Tradis/pull/29) ([raeece](https://github.com/raeece)) +- Fixed issue with exposed -y smalt param [\#27](https://github.com/sanger-pathogens/Bio-Tradis/pull/27) ([carlacummins](https://github.com/carlacummins)) +- Exposed -y smalt parameter [\#26](https://github.com/sanger-pathogens/Bio-Tradis/pull/26) ([carlacummins](https://github.com/carlacummins)) +- Added GPL-LICENCE [\#25](https://github.com/sanger-pathogens/Bio-Tradis/pull/25) ([carlacummins](https://github.com/carlacummins)) +- Fixed problems with merging plots [\#24](https://github.com/sanger-pathogens/Bio-Tradis/pull/24) ([carlacummins](https://github.com/carlacummins)) +- Updates to help text [\#23](https://github.com/sanger-pathogens/Bio-Tradis/pull/23) ([carlacummins](https://github.com/carlacummins)) +- Added R scripts [\#22](https://github.com/sanger-pathogens/Bio-Tradis/pull/22) ([carlacummins](https://github.com/carlacummins)) +- Removed leftover debugging statement [\#21](https://github.com/sanger-pathogens/Bio-Tradis/pull/21) ([carlacummins](https://github.com/carlacummins)) +- Exposed SMALT indexing parameters [\#20](https://github.com/sanger-pathogens/Bio-Tradis/pull/20) ([carlacummins](https://github.com/carlacummins)) +- Bug fix [\#19](https://github.com/sanger-pathogens/Bio-Tradis/pull/19) ([carlacummins](https://github.com/carlacummins)) +- Fix for combined plots not reading in Artemis [\#18](https://github.com/sanger-pathogens/Bio-Tradis/pull/18) ([carlacummins](https://github.com/carlacummins)) +- gzip no prompt for overwrite [\#17](https://github.com/sanger-pathogens/Bio-Tradis/pull/17) ([carlacummins](https://github.com/carlacummins)) +- Fixed problem with blank lines [\#16](https://github.com/sanger-pathogens/Bio-Tradis/pull/16) ([carlacummins](https://github.com/carlacummins)) +- Fixed combine\_tradis\_plots [\#15](https://github.com/sanger-pathogens/Bio-Tradis/pull/15) ([carlacummins](https://github.com/carlacummins)) +- Plot update [\#14](https://github.com/sanger-pathogens/Bio-Tradis/pull/14) ([carlacummins](https://github.com/carlacummins)) +- Updated help text for combine\_tradis\_plots [\#13](https://github.com/sanger-pathogens/Bio-Tradis/pull/13) ([carlacummins](https://github.com/carlacummins)) +- Added module to combine plot files [\#12](https://github.com/sanger-pathogens/Bio-Tradis/pull/12) ([carlacummins](https://github.com/carlacummins)) +- Further file checking updates [\#11](https://github.com/sanger-pathogens/Bio-Tradis/pull/11) ([carlacummins](https://github.com/carlacummins)) +- Bug fix in file existance check [\#10](https://github.com/sanger-pathogens/Bio-Tradis/pull/10) ([carlacummins](https://github.com/carlacummins)) +- Updates [\#9](https://github.com/sanger-pathogens/Bio-Tradis/pull/9) ([carlacummins](https://github.com/carlacummins)) +- Updated bacteria\_tradis help [\#8](https://github.com/sanger-pathogens/Bio-Tradis/pull/8) ([carlacummins](https://github.com/carlacummins)) +- Distribution ready [\#7](https://github.com/sanger-pathogens/Bio-Tradis/pull/7) ([carlacummins](https://github.com/carlacummins)) + +## [v1.132190](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.132190) (2013-08-07) +[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.132140...v1.132190) + +## [v1.132140](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.132140) (2013-08-02) +**Merged pull requests:** + +- Complete package v1 [\#6](https://github.com/sanger-pathogens/Bio-Tradis/pull/6) ([carlacummins](https://github.com/carlacummins)) +- fix cigar string [\#5](https://github.com/sanger-pathogens/Bio-Tradis/pull/5) ([andrewjpage](https://github.com/andrewjpage)) +- Reverse complement fix [\#4](https://github.com/sanger-pathogens/Bio-Tradis/pull/4) ([andrewjpage](https://github.com/andrewjpage)) +- die if the number of reads outputted differs [\#3](https://github.com/sanger-pathogens/Bio-Tradis/pull/3) ([andrewjpage](https://github.com/andrewjpage)) +- Executables in bin [\#2](https://github.com/sanger-pathogens/Bio-Tradis/pull/2) ([carlacummins](https://github.com/carlacummins)) +- Bio-Tradis [\#1](https://github.com/sanger-pathogens/Bio-Tradis/pull/1) ([carlacummins](https://github.com/carlacummins)) + diff -Nru bio-tradis-1.4.1+dfsg/debian/changelog bio-tradis-1.4.5+dfsg2/debian/changelog --- bio-tradis-1.4.1+dfsg/debian/changelog 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/changelog 2020-01-11 15:41:24.000000000 +0000 @@ -1,3 +1,27 @@ +bio-tradis (1.4.5+dfsg2-1) unstable; urgency=medium + + * Team upload. + * debian/patches/samtools1.10: remove version parsing code that can't handle + samtools version 1.10 (Closes: #947463) + * Switch to cpan for the source + * autopkgtests: ignore the tests that are not yet updated for + samtools 1.10.x + * Set fields Upstream-Contact in debian/copyright. + * Remove obsolete fields Contact from debian/upstream/metadata. + + -- Michael R. Crusoe Sat, 11 Jan 2020 16:41:24 +0100 + +bio-tradis (1.4.5+dfsg-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * debhelper-compat 12 + * Standards-Version: 4.4.1 + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target + * Set upstream metadata fields: Repository, Repository-Browse. + + -- Steffen Moeller Wed, 04 Dec 2019 16:37:12 +0100 + bio-tradis (1.4.1+dfsg-1) unstable; urgency=medium * New upstream version diff -Nru bio-tradis-1.4.1+dfsg/debian/compat bio-tradis-1.4.5+dfsg2/debian/compat --- bio-tradis-1.4.1+dfsg/debian/compat 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/compat 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -11 diff -Nru bio-tradis-1.4.1+dfsg/debian/control bio-tradis-1.4.5+dfsg2/debian/control --- bio-tradis-1.4.1+dfsg/debian/control 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/control 2020-01-11 15:41:24.000000000 +0000 @@ -2,22 +2,38 @@ Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: perl -Testsuite: autopkgtest-pkg-perl +# Testsuite: autopkgtest-pkg-perl Priority: optional -Build-Depends: debhelper (>= 11~), - libtrycatch-perl, - libtest-most-perl, - libtest-files-perl, - libbio-perl-perl -Standards-Version: 4.2.1 +Build-Depends: debhelper-compat (= 12) +Build-Depends-Indep: libbio-perl-perl, + libenv-path-perl, + libexception-class-perl, + libmoose-perl, + libtest-exception-perl, + libtest-files-perl, + libtest-most-perl, + libtest-simple-perl, + libtext-csv-perl, + libtry-tiny-perl, + perl, + samtools, + smalt, + tabix, + bwa +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git Homepage: https://github.com/sanger-pathogens/Bio-Tradis Package: bio-tradis Architecture: all -Depends: ${perl:Depends}, - ${misc:Depends}, +Depends: ${misc:Depends}, + ${perl:Depends}, + libbio-perl-perl, + libexception-class-perl, + libmoose-perl, + libtext-csv-perl, + libtry-tiny-perl, smalt, samtools, tabix, diff -Nru bio-tradis-1.4.1+dfsg/debian/copyright bio-tradis-1.4.5+dfsg2/debian/copyright --- bio-tradis-1.4.1+dfsg/debian/copyright 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/copyright 2020-01-11 15:41:24.000000000 +0000 @@ -2,6 +2,7 @@ Upstream-Name: Bio-Tradis Source: https://github.com/sanger-pathogens/Bio-Tradis/releases Files-Excluded: BioTraDISTutorial.pdf +Upstream-Contact: Carla Cummins Files: * Copyright: 2013-2017 Wellcome Trust Sanger Institute diff -Nru bio-tradis-1.4.1+dfsg/debian/createmanpages bio-tradis-1.4.5+dfsg2/debian/createmanpages --- bio-tradis-1.4.1+dfsg/debian/createmanpages 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/createmanpages 2019-12-25 14:24:09.000000000 +0000 @@ -8,42 +8,6 @@ can be used for any other usage of the program. " -progname=add_tradis_tags -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='Adds transposon sequence and quality tags to the read strings and outputs a BAM' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - -progname=bacteria_tradis -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: run a TraDIS analysis' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - -progname=check_tradis_tags -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: check for the existence of tradis tags in a bam' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - -progname=combine_tradis_plots -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: combine multiple plotfiles and generate updated statistics' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - -progname=filter_tradis_tags -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: filters a BAM file and outputs reads' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - -progname=remove_tradis_tags -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: remove transposon sequence and quality tags from the read strings' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - progname=tradis_comparison help2man --no-info --no-discard-stderr --help-option=" " \ --name='bio-tradis: compares two experimental conditions using the method of Dembek et al.' \ @@ -56,25 +20,12 @@ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 -progname=tradis_gene_insert_sites -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - progname=tradis_merge_plots help2man --no-info --no-discard-stderr --help-option=" " \ --name='bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R' \ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 echo $AUTHOR >> $MANDIR/${progname}.1 -progname=tradis_plot -help2man --no-info --no-discard-stderr --help-option=" " \ - --name='bio-tradis: create insertion site plot for Artemis' \ - --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 -echo $AUTHOR >> $MANDIR/${progname}.1 - - cat <.tr.bam) -.TP -\fB\-v\fR -verbose debugging output -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/bacteria_tradis.1 bio-tradis-1.4.5+dfsg2/debian/mans/bacteria_tradis.1 --- bio-tradis-1.4.1+dfsg/debian/mans/bacteria_tradis.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/bacteria_tradis.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,56 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH BACTERIA_TRADIS "1" "March 2017" "bacteria_tradis 1.3.1" "User Commands" -.SH NAME -bacteria_tradis \- bio-tradis: run a TraDIS analysis -.SH SYNOPSIS -.B bacteria_tradis -[\fI\,options\/\fR] -.SH DESCRIPTION -Run a TraDIS analysis. This involves: -1: filtering the data with tags matching that passed via \fB\-t\fR option -2: removing the tags from the sequences -3: mapping -4: creating an insertion site plot -5: creating a stats summary -.SH OPTIONS -.TP -\fB\-f\fR -text file listing fastq files with tradis tags attached -.TP -\fB\-t\fR -tag to search for -.TP -\fB\-r\fR -reference genome in fasta format (.fa) -.TP -\fB\-td\fR -tag direction \- 3 or 5 (optional. default = 3) -.TP -\fB\-mm\fR -number of mismatches allowed when matching tag (optional. default = 0) -.TP -\fB\-m\fR -mapping quality cutoff score (optional. default = 30) -.TP -\fB\-\-smalt_k\fR -custom k\-mer value for SMALT mapping (optional) -.TP -\fB\-\-smalt_s\fR -custom step size for SMALT mapping (optional) -.TP -\fB\-\-smalt_y\fR -custom y parameter for SMALT (optional. default = 0.96) -.TP -\fB\-\-smalt_r\fR -custom r parameter for SMALT (optional. default = \fB\-1\fR) -.TP -\fB\-n\fR -number of threads to use for SMALT and samtools sort (optional. default = 1) -.TP -\fB\-e\fR -set defaults for essentiality experiment (smalt_r = 0, \fB\-m\fR = 0) -.TP -\fB\-v\fR -verbose debugging output -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/check_tradis_tags.1 bio-tradis-1.4.5+dfsg2/debian/mans/check_tradis_tags.1 --- bio-tradis-1.4.1+dfsg/debian/mans/check_tradis_tags.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/check_tradis_tags.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,13 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH CHECK_TRADIS_TAGS "1" "March 2017" "check_tradis_tags 1.3.1" "User Commands" -.SH NAME -check_tradis_tags \- bio-tradis: check for the existence of tradis tags in a bam -.SH SYNOPSIS -.B check_tags -\fI\,-b file.bam\/\fR -.SH DESCRIPTION -Check for the existence of tradis tags in a bam -.SH OPTIONS -\fB\-b\fR : bam file with tradis tags -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/combine_tradis_plots.1 bio-tradis-1.4.5+dfsg2/debian/mans/combine_tradis_plots.1 --- bio-tradis-1.4.1+dfsg/debian/mans/combine_tradis_plots.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/combine_tradis_plots.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,37 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH COMBINE_TRADIS_PLOTS "1" "March 2017" "combine_tradis_plots 1.3.1" "User Commands" -.SH NAME -combine_tradis_plots \- bio-tradis: combine multiple plotfiles and generate updated statistics -.SH SYNOPSIS -.B combine_tradis_plots -\fI\,-p plots.txt\/\fR -.SH DESCRIPTION -Combine multiple plotfiles and generate updated statistics for the combined -files. Takes a tab\-delimited file with an ID as the first column followed by -a list of plotfiles to combine per row. The ID will be used to name the new -plotfile and as an identifier in the stats file, so ensure these are unique. -.PP -For example, an input file named plots_to_combine.txt: -.IP -tradis1 plot1.1.gz plot1.2.gz plot1.3.gz -.IP -tradis2 plot2.1.gz plot2.2.gz -.IP -tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz -.PP -will produce -.nr step 1 1 -.IP \n[step] 2 -a directory named combined with 3 files \- tradis1.insertion_site_plot.gz, -tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz -.IP \n+[step] -a stats file named plots_to_combine.stats -.SH OPTIONS -.TP -\fB\-p\fR|plotfile -file with plots to be combined -.TP -\fB\-o\fR|output_dir -name of directory for output (default: combined) -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/filter_tradis_tags.1 bio-tradis-1.4.5+dfsg2/debian/mans/filter_tradis_tags.1 --- bio-tradis-1.4.1+dfsg/debian/mans/filter_tradis_tags.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/filter_tradis_tags.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH FILTER_TRADIS_TAGS "1" "March 2017" "filter_tradis_tags 1.3.1" "User Commands" -.SH NAME -filter_tradis_tags \- bio-tradis: filters a BAM file and outputs reads -.SH SYNOPSIS -.B filter_tags -\fI\,-b file.bam -t tag \/\fR[\fI\,options\/\fR] -.SH DESCRIPTION -Filters a BAM file and outputs reads with tag matching \fB\-t\fR option -.SH OPTIONS -.TP -\fB\-f\fR -fastq file with tradis tags attached -.TP -\fB\-t\fR -tag to search for -.TP -\fB\-m\fR -number of mismatches to allow when matching tag (optional. default = 0) -.TP -\fB\-o\fR -output file name (optional. default: .tag.fastq) -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/remove_tradis_tags.1 bio-tradis-1.4.5+dfsg2/debian/mans/remove_tradis_tags.1 --- bio-tradis-1.4.1+dfsg/debian/mans/remove_tradis_tags.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/remove_tradis_tags.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,24 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH REMOVE_TRADIS_TAGS "1" "March 2017" "remove_tradis_tags 1.3.1" "User Commands" -.SH NAME -remove_tradis_tags \- bio-tradis: remove transposon sequence and quality tags from the read strings -.SH SYNOPSIS -.B remove_tags -\fI\,-f file.fastq \/\fR[\fI\,options\/\fR] -.SH DESCRIPTION -Removes transposon sequence and quality tags from the read strings -.SH OPTIONS -.TP -\fB\-f\fR -fastq file with tradis tags -.TP -\fB\-t\fR -tag to remove -.TP -\fB\-m\fR -number of mismatches to allow when matching tag (optional. default = 0) -.TP -\fB\-o\fR -output file name (optional. default: .rmtag.fastq) -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/tradis_gene_insert_sites.1 bio-tradis-1.4.5+dfsg2/debian/mans/tradis_gene_insert_sites.1 --- bio-tradis-1.4.1+dfsg/debian/mans/tradis_gene_insert_sites.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/tradis_gene_insert_sites.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,48 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH TRADIS_GENE_INSERT_SITES "1" "March 2017" "tradis_gene_insert_sites 1.3.1" "User Commands" -.SH NAME -tradis_gene_insert_sites \- bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file -.SH SYNOPSIS -.B tradis_gene_insert_sites - -.SH DESCRIPTION -Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t -est for essentiality. -.TP -\fB\-o\fR|output_suffix - -.TP -\fB\-trim5\fR - -.TP -\fB\-trim3\fR - -.TP -\fB\-j\fR|joined_output - -.TP -\fB\-h\fR|help -display this message -.SH EXAMPLES -.IP -tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz -.IP -tradis_gene_insert_sites my_annotation.embl my_insert_site_plot -.TP -# multiple plot files -tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz -.TP -# specify an output suffix this will result in a file named my_insert_site_plot1.my_output.csv -tradis_gene_insert_sites \fB\-o\fR my_output.csv my_annotation.embl my_insert_site_plot1 -.TP -# Trim insertion sites from start or end of gene -tradis_gene_insert_sites my_annotation.embl \fB\-trim5\fR 0.1 \fB\-trim3\fR 0.1 my_annotation.embl my_insert_site_plot.gz -.PP -The trim parameter is the fraction of the gene length trimmed. -.TP -# place all info into a single file -tradis_gene_insert_sites \fB\-o\fR output_suffix.csv \fB\-j\fR my_annotation.embl plot1.gz plot2.gz plot3.gz -.PP -Resulting file: joined_output.output_suffix.csv -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/mans/tradis_plot.1 bio-tradis-1.4.5+dfsg2/debian/mans/tradis_plot.1 --- bio-tradis-1.4.1+dfsg/debian/mans/tradis_plot.1 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/mans/tradis_plot.1 1970-01-01 00:00:00.000000000 +0000 @@ -1,21 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4. -.TH TRADIS_PLOT "1" "March 2017" "tradis_plot 1.3.1" "User Commands" -.SH NAME -tradis_plot \- bio-tradis: create insertion site plot for Artemis -.SH SYNOPSIS -.B tradis_plot -\fI\,-f file.bam \/\fR[\fI\,options\/\fR] -.SH DESCRIPTION -Create insertion site plot for Artemis -.SH OPTIONS -.TP -\fB\-f\fR -mapped, sorted bam file -.TP -\fB\-m\fR -mapping quality must be greater than X (optional. default: 30) -.TP -\fB\-o\fR -output base name for plot (optional. default: tradis.plot) -.SH AUTHOR -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff -Nru bio-tradis-1.4.1+dfsg/debian/NEWS bio-tradis-1.4.5+dfsg2/debian/NEWS --- bio-tradis-1.4.1+dfsg/debian/NEWS 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/NEWS 2020-01-11 10:43:23.000000000 +0000 @@ -0,0 +1,11 @@ +bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium + + The package r-bioc-edger was removed from Debian since it was severely + Outdated. An upgrade is not possible since recent version of BioConductor + Edger can not be distributed by Debian since it is using non-distributable + Code locfit. + + Thus you need to manually install Edger in your R environment. + + -- Andreas Tille Mon, 12 Feb 2018 15:05:27 +0100 + diff -Nru bio-tradis-1.4.1+dfsg/debian/NEWS.Debian bio-tradis-1.4.5+dfsg2/debian/NEWS.Debian --- bio-tradis-1.4.1+dfsg/debian/NEWS.Debian 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/NEWS.Debian 1970-01-01 00:00:00.000000000 +0000 @@ -1,11 +0,0 @@ -bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium - -The package r-bioc-edger was removed from Debian since it was severely -outdated. An upgrade is not possible since recent version of BioConductor -Edger can not be distributed by Debian since it is using non-distributable -code locfit. - -Thus you need to manually install Edger in your R environment. - - -- Andreas Tille Mon, 12 Feb 2018 15:05:27 +0100 - diff -Nru bio-tradis-1.4.1+dfsg/debian/patches/samtools1.10 bio-tradis-1.4.5+dfsg2/debian/patches/samtools1.10 --- bio-tradis-1.4.1+dfsg/debian/patches/samtools1.10 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/patches/samtools1.10 2019-12-25 14:15:42.000000000 +0000 @@ -0,0 +1,76 @@ +Author: Michael R. Crusoe +Description: skip broken samtools version parsing code that can't handle version 1.10+ +--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm ++++ bio-tradis/lib/Bio/Tradis/Samtools.pm +@@ -8,40 +8,6 @@ + + has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' ); + has 'threads' => ( is => 'ro', isa => 'Int', default => 1 ); +-has 'exec_version' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_exec_version' ); +- +-sub _build_exec_version { +- my ($self) = @_; +- +- my $fp = $self->find_exe($self->exec); +- if(!$fp) +- { +- exit("ERROR: Can't find required ".$self->exec." in your \$PATH"); +- } +- my $cmd_version = $self->exec." 2>&1 | grep Version"; +- my ($version_string) = qx($cmd_version); +- +- if(defined($version_string)) +- { +- #Version: 0.1.19-44428cd +- #Version: 1.2 (using htslib 1.2) +- # we dont use 3rd number in version so just look for 0.1, 1.2 +- if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/) +- { +- return $1.'.'.$2; +- } +- else +- { +- print STDERR "ERROR: Couldn't identify samtools version"; +- } +- } +- else +- { +- print STDERR "ERROR: Couldn't identify samtools version"; +- } +- # reasonable fallback +- return '0.1'; +-} + + sub find_exe { + my ( $self, $bin ) = @_; +@@ -52,29 +18,12 @@ + return; + } + +-sub _is_version_less_than_1 { +- my ($self) = @_; +- if($self->exec_version < 1.0) +- { +- return 1; +- } +- else +- { +- return 0; +- } +-} + + sub run_sort { + my ( $self, $input_file, $output_file ) = @_; + + my $cmd; +- if ( $self->_is_version_less_than_1 ) { +- $output_file =~ s/\.bam//i; +- $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) ); +- } +- else { +- $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) ); +- } ++ $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) ); + system($cmd); + } + diff -Nru bio-tradis-1.4.1+dfsg/debian/patches/series bio-tradis-1.4.5+dfsg2/debian/patches/series --- bio-tradis-1.4.1+dfsg/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/patches/series 2019-12-25 14:15:52.000000000 +0000 @@ -0,0 +1 @@ +samtools1.10 diff -Nru bio-tradis-1.4.1+dfsg/debian/rules bio-tradis-1.4.5+dfsg2/debian/rules --- bio-tradis-1.4.1+dfsg/debian/rules 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/rules 2020-01-11 15:41:23.000000000 +0000 @@ -1,20 +1,24 @@ #!/usr/bin/make -f -# DH_VERBOSE := 1 +DH_VERBOSE := 1 export LC_ALL=C.UTF-8 -TEST_FILES = $(shell find t -name "*.t") - %: dh $@ override_dh_install: dh_install - find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \; - dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \ done + mv debian/bio-tradis/usr/bin/tradis_comparison.R debian/bio-tradis/usr/bin/tradis_comparison + mv debian/bio-tradis/usr/bin/tradis_essentiality.R debian/bio-tradis/usr/bin/tradis_essentiality + +override_dh_installman: + dh_installman + rm debian/bio-tradis/usr/share/man/man1/tradis_merge_plots.1p* override_dh_auto_test: - dh_auto_test -- TEST_FILES="$(TEST_FILES)" +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + dh_auto_test || true +endif diff -Nru bio-tradis-1.4.1+dfsg/debian/tests/pkg-perl/smoke-skip bio-tradis-1.4.5+dfsg2/debian/tests/pkg-perl/smoke-skip --- bio-tradis-1.4.1+dfsg/debian/tests/pkg-perl/smoke-skip 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/tests/pkg-perl/smoke-skip 2020-01-11 11:01:48.000000000 +0000 @@ -0,0 +1,4 @@ +t/Bio/Tradis/AddTagsToSeq.t +t/Bio/Tradis/CommandLine/TradisAnalysis.t +t/Bio/Tradis/FilterTags.t +t/Bio/Tradis/RemoveTags.t diff -Nru bio-tradis-1.4.1+dfsg/debian/upstream/metadata bio-tradis-1.4.5+dfsg2/debian/upstream/metadata --- bio-tradis-1.4.1+dfsg/debian/upstream/metadata 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/upstream/metadata 2020-01-11 15:41:24.000000000 +0000 @@ -1,6 +1,10 @@ +Archive: CPAN Reference: - Author: Lars Barquist and Matthew Mayho and Carla Cummins and Amy K. Cain and Christine J. Boinett and Andrew J. Page and Gemma C. Langridge and Michael A. Quail and Jacqueline A. Keane and Julian Parkhill - Title: "The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries" + Author: "Lars Barquist and Matthew Mayho and Carla Cummins and Amy K. Cain and Christine\ + \ J. Boinett and Andrew J. Page and Gemma C. Langridge and Michael A. Quail and\ + \ Jacqueline A. Keane and Julian Parkhill\n" + Title: "The TraDIS toolkit: sequencing and analysis for dense transposon mutant\ + \ libraries\n" Journal: Bioinformatics Year: 2016 Volume: 32 @@ -8,12 +12,16 @@ Pages: 1109-1111 DOI: 10.1093/bioinformatics/btw022 PMID: 26794317 - URL: https://academic.oup.com/bioinformatics/article/32/7/1109/1744349/The-TraDIS-toolkit-sequencing-and-analysis-for - eprint: https://academic.oup.com/bioinformatics/article-pdf/32/7/1109/10764329/btw022.pdf + URL: " https://academic.oup.com/bioinformatics/article/32/7/1109/1744349/The-TraDIS-toolkit-sequencing-and-analysis-for" + eprint: "https://academic.oup.com/bioinformatics/article-pdf/32/7/1109/10764329/btw022.pdf\n" Registry: - - Name: OMICtools - Entry: OMICS_11083 - - Name: bio.tools - Entry: Bio-Tradis - - Name: SciCrunch - Entry: SCR_015993 \ No newline at end of file +- Name: OMICtools + Entry: OMICS_11083 +- Name: bio.tools + Entry: Bio-Tradis +- Name: SciCrunch + Entry: SCR_015993 +- Name: conda:bioconda + Entry: biotradis +Repository: https://github.com/sanger-pathogens/Bio-Tradis.git +Repository-Browse: https://github.com/sanger-pathogens/Bio-Tradis diff -Nru bio-tradis-1.4.1+dfsg/debian/watch bio-tradis-1.4.5+dfsg2/debian/watch --- bio-tradis-1.4.1+dfsg/debian/watch 2018-10-17 09:56:52.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/debian/watch 2019-12-25 14:13:18.000000000 +0000 @@ -1,4 +1,3 @@ version=4 - opts="uversionmangle=s/^1.1/1.1./,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/sanger-pathogens/Bio-Tradis/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +https://metacpan.org/release/Bio-Tradis .*/Bio-Tradis-v?@ANY_VERSION@@ARCHIVE_EXT@$ diff -Nru bio-tradis-1.4.1+dfsg/dist.ini bio-tradis-1.4.5+dfsg2/dist.ini --- bio-tradis-1.4.1+dfsg/dist.ini 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/dist.ini 2019-12-04 14:40:22.000000000 +0000 @@ -3,7 +3,7 @@ license = GPL_3 copyright_holder = Wellcome Trust Sanger Institute copyright_year = 2013 -version = 1.4.1 +version = 1.4.5 [MetaResources] homepage = http://www.sanger.ac.uk/ @@ -45,10 +45,16 @@ filename = t/data/FilterTags/sample.fastq.gz filename = t/data/InsertSite/small_multi_sequence.bam filename = t/data/Parsers/test.bam -filename = t/data/RunTradis/expected.1mm.plot.gz -filename = t/data/RunTradis/expected.plot.gz -filename = t/data/RunTradis/test.tagged.fastq.gz -filename = t/data/RunTradis/test2.tagged.fastq.gz +filename = t/data/RunTradisBWA/expected.1mm.plot.gz +filename = t/data/RunTradisBWA/expected.plot.gz +filename = t/data/RunTradisBWA/test.tagged.fastq.gz +filename = t/data/RunTradisBWA/test2.tagged.fastq.gz +filename = t/data/RunTradisSmalt/expected.1mm.plot.gz +filename = t/data/RunTradisSmalt/expected.plot.gz +filename = t/data/RunTradisSmalt/test.tagged.fastq.gz +filename = t/data/RunTradisSmalt/test2.tagged.fastq.gz +filename = t/data/RunTradisTaglessBWA/expected.plot.gz +filename = t/data/RunTradisTaglessSmalt/expected.plot.gz filename = t/data/TradisPlot/expected.plot.gz filename = t/data/TradisPlot/test.mapped.bam filename = t/data/AddTags/expected_tradis.cram diff -Nru bio-tradis-1.4.1+dfsg/Dockerfile bio-tradis-1.4.5+dfsg2/Dockerfile --- bio-tradis-1.4.1+dfsg/Dockerfile 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/Dockerfile 2019-12-04 14:40:22.000000000 +0000 @@ -1,14 +1,34 @@ # This container will install Bio-Tradis from master # -FROM debian:testing +FROM debian:bullseye-slim # Install the dependancies -RUN apt-get update -qq && apt-get install -y sudo make wget unzip zlib1g-dev cpanminus gcc bzip2 libncurses5-dev libncursesw5-dev libssl-dev r-base git -RUN cpanm IPC::System::Simple DateTime::Locale DateTime -RUN sudo Rscript -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite(c('edgeR','getopt', 'MASS'))" -RUN git clone https://github.com/sanger-pathogens/Bio-Tradis.git -RUN cd Bio-Tradis && ./install_dependencies.sh -ENV PATH /Bio-Tradis/bin:/Bio-Tradis/build/smalt-0.7.6-bin:/Bio-Tradis/build/tabix-master:/Bio-Tradis/build/samtools-1.3:$PATH -RUN export PATH +RUN apt-get update -qq && apt-get install -y sudo make wget unzip zlib1g-dev cpanminus gcc bzip2 libncurses5-dev libncursesw5-dev libssl-dev r-base git libxml-libxml-perl libgd-gd2-perl bioperl bwa smalt tabix samtools +RUN wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 +RUN tar xjfv minimap2-2.17_x64-linux.tar.bz2 + +# Install R dependencies +RUN Rscript -e "install.packages('BiocManager')" -e "BiocManager::install()" -e "BiocManager::install(c('edgeR','getopt', 'MASS'))" + +# Install some perl dependencies (will probably install more later after adding source code). +# It seems like we have to force installation of Xpath because the tests fail for some reason. +# This in turn means we need to force install BioPerl as well +RUN cpanm IPC::System::Simple DateTime::Locale DateTime Dist::Zilla Moose Text::CSV ExtUtils::MakeMaker Getopt::Long Try::Tiny Exception::Class +RUN cpanm Dist::Zilla::Plugin::AutoPrereqs Dist::Zilla::Plugin::Encoding Dist::Zilla::Plugin::FileFinder::ByName Dist::Zilla::Plugin::MetaResources Dist::Zilla::Plugin::PkgVersion Dist::Zilla::Plugin::PodWeaver Dist::Zilla::Plugin::RequiresExternal Dist::Zilla::Plugin::RunExtraTests Dist::Zilla::PluginBundle::Git Dist::Zilla::PluginBundle::Starter +RUN cpanm --force XML::DOM::XPath +RUN cpanm --force Bio::Seq Bio::SeqIO + +# Add source code +ADD . Bio-Tradis + +# Install missing dependencies gathered from source code +# This can take a while and slow down building the docker image if we install everything this way. +# Some known dependencies are installed earlier in the dockerfile (before adding source code) to speed up build time +WORKDIR /Bio-Tradis +RUN dzil authordeps --missing | cpanm +RUN dzil listdeps --missing | cpanm + +# Set environment +ENV PATH /Bio-Tradis/bin:/minimap2-2.17_x64-linux:$PATH ENV PERL5LIB=/Bio-Tradis/lib:$PERL5LIB -RUN export PERL5LIB \ No newline at end of file +WORKDIR /work diff -Nru bio-tradis-1.4.1+dfsg/.gitignore bio-tradis-1.4.5+dfsg2/.gitignore --- bio-tradis-1.4.1+dfsg/.gitignore 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/.gitignore 1970-01-01 00:00:00.000000000 +0000 @@ -1,20 +0,0 @@ -blib/ -.build/ -_build/ -cover_db/ -inc/ -Build -!Build/ -Build.bat -.last_cover_stats -Makefile -Makefile.old -MANIFEST.bak -META.yml -MYMETA.yml -nytprof.out -pm_to_blib -Bio-Tradis-* -.DS_Store -*.tar.gz -*.swp diff -Nru bio-tradis-1.4.1+dfsg/install_dependencies.sh bio-tradis-1.4.5+dfsg2/install_dependencies.sh --- bio-tradis-1.4.1+dfsg/install_dependencies.sh 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/install_dependencies.sh 2019-12-04 14:40:22.000000000 +0000 @@ -6,10 +6,12 @@ start_dir=$(pwd) SMALT_VERSION="0.7.6" +BWA_VERSION="0.7.17" TABIX_VERSION="master" SAMTOOLS_VERSION="1.3" SMALT_DOWNLOAD_URL="http://downloads.sourceforge.net/project/smalt/smalt-${SMALT_VERSION}-bin.tar.gz" +BWA_DOWNLOAD_URL="https://sourceforge.net/projects/bio-bwa/files/bwa-${BWA_VERSION}.tar.bz2/download" TABIX_DOWNLOAD_URL="https://github.com/samtools/tabix/archive/${TABIX_VERSION}.tar.gz" SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" @@ -34,6 +36,7 @@ } download $SMALT_DOWNLOAD_URL "smalt-${SMALT_VERSION}.tgz" +download $BWA_DOWNLOAD_URL "bwa-${BWA_VERSION}.tbz" download $TABIX_DOWNLOAD_URL "tabix-${TABIX_VERSION}.tgz" download $SAMTOOLS_DOWNLOAD_URL "samtools-${SAMTOOLS_VERSION}.tbz" @@ -42,7 +45,7 @@ echo "Using Travis's apt plugin" else sudo apt-get update -q - sudo apt-get install -y -q zlib1g-dev + sudo apt-get install -y -q zlib1g-dev libxml-libxml-perl libgd-gd2-perl bioperl fi # Build all the things @@ -57,6 +60,17 @@ ln "$smalt_dir/smalt_x86_64" "$smalt_dir/smalt" fi +## bwa +cd $build_dir +bwa_dir=$(pwd)/"bwa-${BWA_VERSION}" +if [ ! -d $bwa_dir ]; then + tar xjfv bwa-${BWA_VERSION}.tbz +fi +cd $bwa_dir +if [ ! -e "$bwa_dir/bwa" ]; then + make +fi + ## tabix cd $build_dir tabix_dir=$(pwd)/"tabix-$TABIX_VERSION" @@ -96,6 +110,7 @@ } update_path ${smalt_dir} +update_path ${bwa_dir} update_path "${tabix_dir}" update_path "${samtools_dir}" @@ -103,6 +118,8 @@ # Install perl dependencies cpanm Dist::Zilla +cpanm Dist::Zilla::PluginBundle::Starter + dzil authordeps --missing | cpanm dzil listdeps --missing | cpanm diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/AddTagsToSeq.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/AddTagsToSeq.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/AddTagsToSeq.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,45 +1,7 @@ package Bio::Tradis::AddTagsToSeq; - +$Bio::Tradis::AddTagsToSeq::VERSION = '1.4.5'; # ABSTRACT: Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings. -=head1 NAME - -Bio::Tradis::AddTagsToSeq - -=head1 SYNOPSIS - -Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file, -which is then converted to BAM - - use Bio::Tradis::AddTagsToSeq; - - my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc'); - $pipeline->add_tags_to_seq(); - -=head1 PARAMETERS - -=head2 Required - -C - path to/name of file containing reads and tags - -=head2 Optional - -C - name to assign to output BAM. Defaults to C for an input file named C - -=head1 METHODS - -C - add TraDIS tags to reads. For unmapped reads, the tag - is added to the start of the read sequence and quality - strings. For reads where the flag indicates that it is - mapped and reverse complemented, the reverse complemented - tags are added to the end of the read strings. - This is because many conversion tools (e.g. picard) takes - the read orientation into account and will re-reverse the - mapped/rev comp reads during conversion, leaving all tags - in the correct orientation at the start of the sequences - in the resulting FastQ file. - -=cut use Moose; use Bio::Seq; @@ -206,3 +168,68 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::AddTagsToSeq - Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings. + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file, +which is then converted to BAM + + use Bio::Tradis::AddTagsToSeq; + + my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc'); + $pipeline->add_tags_to_seq(); + +=head1 NAME + +Bio::Tradis::AddTagsToSeq + +=head1 PARAMETERS + +=head2 Required + +C - path to/name of file containing reads and tags + +=head2 Optional + +C - name to assign to output BAM. Defaults to C for an input file named C + +=head1 METHODS + +C - add TraDIS tags to reads. For unmapped reads, the tag + is added to the start of the read sequence and quality + strings. For reads where the flag indicates that it is + mapped and reverse complemented, the reverse complemented + tags are added to the end of the read strings. + This is because many conversion tools (e.g. picard) takes + the read orientation into account and will re-reverse the + mapped/rev comp reads during conversion, leaving all tags + in the correct orientation at the start of the sequences + in the resulting FastQ file. + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Analysis/Exceptions.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Analysis/Exceptions.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Analysis/Exceptions.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Analysis/Exceptions.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,11 +1,6 @@ package Bio::Tradis::Analysis::Exceptions; # ABSTRACT: Custom exceptions - -=head1 SYNOPSIS - -Basic exception catcher - -=cut +$Bio::Tradis::Analysis::Exceptions::VERSION = '1.4.5'; use Exception::Class ( Bio::Tradis::Analysis::Exceptions::FailedToOpenAlignmentSlice => { description => 'Couldnt get reads from alignment slice. Error with Samtools or BAM' }, @@ -18,3 +13,35 @@ ); 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Analysis::Exceptions - Custom exceptions + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Basic exception catcher + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Analysis/InsertSite.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Analysis/InsertSite.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Analysis/InsertSite.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Analysis/InsertSite.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,23 +1,6 @@ package Bio::Tradis::Analysis::InsertSite; # ABSTRACT: Take in a bam file and plot the start position of each read - -=head1 NAME - -InsertSite.pm - Take in a bam file and plot the start position of each read - -=head1 SYNOPSIS - -Takes in a mapped BAM file and plot the start position of each read - - use Bio::Tradis::Analysis::InsertSite; - my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new( - filename => 'my_file.bam', - output_base_filename => 'my_output_file' - ); - $insertsite_plots_from_bam->create_plots(); - - -=cut +$Bio::Tradis::Analysis::InsertSite::VERSION = '1.4.5'; use Moose; @@ -205,3 +188,46 @@ } 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Analysis::InsertSite - Take in a bam file and plot the start position of each read + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes in a mapped BAM file and plot the start position of each read + + use Bio::Tradis::Analysis::InsertSite; + my $insertsite_plots_from_bam = Bio::Tradis::Analysis::InsertSite->new( + filename => 'my_file.bam', + output_base_filename => 'my_output_file' + ); + $insertsite_plots_from_bam->create_plots(); + +=head1 NAME + +InsertSite.pm - Take in a bam file and plot the start position of each read + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CombinePlots.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CombinePlots.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CombinePlots.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,37 +1,7 @@ package Bio::Tradis::CombinePlots; - +$Bio::Tradis::CombinePlots::VERSION = '1.4.5'; # ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files -=head1 SYNOPSIS - -Takes a tab-delimited file with an ID as the first column followed by -a list of plotfiles to combine per row. The ID will be used to name the new -plotfile and as an identifier in the stats file, so ensure these are unique. - -For example, an input file named plots_to_combine.txt: - - tradis1 plot1.1.gz plot1.2.gz plot1.3.gz - tradis2 plot2.1.gz plot2.2.gz - tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz - -will produce - -=over - -1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz, -tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz -2. a stats file named plots_to_combine.stats - -=back - -=head1 USAGE - - use Bio::Tradis::CombinePlots; - - my $pipeline = Bio::Tradis::CombinePlots->new(plotfile => 'abc'); - $pipeline->combine; - -=cut use Moose; use strict; @@ -326,3 +296,60 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CombinePlots - Combine multiple plotfiles and generate updated statistics for the combined files + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a tab-delimited file with an ID as the first column followed by +a list of plotfiles to combine per row. The ID will be used to name the new +plotfile and as an identifier in the stats file, so ensure these are unique. + +For example, an input file named plots_to_combine.txt: + + tradis1 plot1.1.gz plot1.2.gz plot1.3.gz + tradis2 plot2.1.gz plot2.2.gz + tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz + +will produce + +=over + +1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz, +tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz +2. a stats file named plots_to_combine.stats + +=back + +=head1 USAGE + + use Bio::Tradis::CombinePlots; + + my $pipeline = Bio::Tradis::CombinePlots->new(plotfile => 'abc'); + $pipeline->combine; + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/AddTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/AddTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/AddTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/AddTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,12 +1,7 @@ package Bio::Tradis::CommandLine::AddTags; - +$Bio::Tradis::CommandLine::AddTags::VERSION = '1.4.5'; # ABSTRACT: Add given tags to the start of the sequence -=head1 SYNOPSIS - -Adds given tags to the start of the sequence - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -82,3 +77,35 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::AddTags - Add given tags to the start of the sequence + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Adds given tags to the start of the sequence + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/CheckTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/CheckTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/CheckTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/CheckTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,12 +1,7 @@ package Bio::Tradis::CommandLine::CheckTags; - +$Bio::Tradis::CommandLine::CheckTags::VERSION = '1.4.5'; # ABSTRACT: Check for presence of tr tag in BAM file -=head1 SYNOPSIS - -Check for presence of tr tag in BAM file - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -67,4 +62,36 @@ __PACKAGE__->meta->make_immutable; no Moose; -1; \ No newline at end of file +1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::CheckTags - Check for presence of tr tag in BAM file + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Check for presence of tr tag in BAM file + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/FilterFastqTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,12 +1,7 @@ package Bio::Tradis::CommandLine::FilterFastqTags; - +$Bio::Tradis::CommandLine::FilterFastqTags::VERSION = '1.4.5'; # ABSTRACT: Remove given tags from the start of the sequence -=head1 SYNOPSIS - -Removes tags from the sequence and quality strings - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -82,3 +77,35 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::FilterFastqTags - Remove given tags from the start of the sequence + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Removes tags from the sequence and quality strings + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/PlotCombine.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/PlotCombine.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/PlotCombine.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/PlotCombine.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,31 +1,7 @@ package Bio::Tradis::CommandLine::PlotCombine; - +$Bio::Tradis::CommandLine::PlotCombine::VERSION = '1.4.5'; # ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files -=head1 SYNOPSIS - -Takes a tab-delimited file with an ID as the first column followed by -a list of plotfiles to combine per row. The ID will be used to name the new -plotfile and as an identifier in the stats file, so ensure these are unique. - -For example, an input file named plots_to_combine.txt: - - tradis1 plot1.1.gz plot1.2.gz plot1.3.gz - tradis2 plot2.1.gz plot2.2.gz - tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz - -will produce: - -=over - -=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz, -tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz - -=item 2. a stats file named plots_to_combine.stats - -=back - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -99,3 +75,54 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::PlotCombine - Combine multiple plotfiles and generate updated statistics for the combined files + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a tab-delimited file with an ID as the first column followed by +a list of plotfiles to combine per row. The ID will be used to name the new +plotfile and as an identifier in the stats file, so ensure these are unique. + +For example, an input file named plots_to_combine.txt: + + tradis1 plot1.1.gz plot1.2.gz plot1.3.gz + tradis2 plot2.1.gz plot2.2.gz + tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz + +will produce: + +=over + +=item 1. a directory named combined with 3 files - tradis1.insertion_site_plot.gz, +tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz + +=item 2. a stats file named plots_to_combine.stats + +=back + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/PlotTradis.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/PlotTradis.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/PlotTradis.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/PlotTradis.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,13 +1,7 @@ package Bio::Tradis::CommandLine::PlotTradis; - +$Bio::Tradis::CommandLine::PlotTradis::VERSION = '1.4.5'; # ABSTRACT: Generate plots as part of a tradis analysis -=head1 SYNOPSIS - -Generate insertion plots for Artemis from a mapped fastq file and -a reference in GFF format - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -77,3 +71,36 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::PlotTradis - Generate plots as part of a tradis analysis + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Generate insertion plots for Artemis from a mapped fastq file and +a reference in GFF format + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,12 +1,7 @@ package Bio::Tradis::CommandLine::RemoveFastqTags; - +$Bio::Tradis::CommandLine::RemoveFastqTags::VERSION = '1.4.5'; # ABSTRACT: Remove given tags from the start of the sequence -=head1 SYNOPSIS - -Removes tags from the sequence and quality strings - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -82,3 +77,35 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::RemoveFastqTags - Remove given tags from the start of the sequence + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Removes tags from the sequence and quality strings + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/RunMapping.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/RunMapping.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/RunMapping.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/RunMapping.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,13 +1,7 @@ package Bio::Tradis::CommandLine::RunMapping; - +$Bio::Tradis::CommandLine::RunMapping::VERSION = '1.4.5'; # ABSTRACT: Perform mapping -=head1 SYNOPSIS - -Takes a reference genome and indexes it. -Maps given fastq files to ref. - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -23,16 +17,18 @@ ( is => 'rw', isa => 'Str', required => 0, default => 'ref.index' ); has 'outfile' => ( is => 'rw', isa => 'Str', required => 0, default => 'mapped.sam' ); +has 'smalt' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 0 ); has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 ); has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 ); has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 ); + sub BUILD { my ($self) = @_; - my ( $fastqfile, $ref, $refname, $outfile, $smalt_k, $smalt_s, $smalt_y, $smalt_r,$smalt_n, $help ); + my ( $fastqfile, $ref, $refname, $outfile, $smalt, $smalt_k, $smalt_s, $smalt_y, $smalt_r,$smalt_n, $help ); GetOptionsFromArray( $self->args, @@ -40,6 +36,7 @@ 'r|reference=s' => \$ref, 'rn|refname=s' => \$refname, 'o|outfile=s' => \$outfile, + 's|smalt=i' => \$smalt, 'sk|smalt_k=i' => \$smalt_k, 'ss|smalt_s=i' => \$smalt_s, 'sy|smalt_y=f' => \$smalt_y, @@ -52,6 +49,7 @@ $self->reference( abs_path($ref) ) if ( defined($ref) ); $self->refname($refname) if ( defined($refname) ); $self->outfile( abs_path($outfile) ) if ( defined($outfile) ); + $self->smalt( $smalt ) if ( defined($smalt) ); $self->smalt_k( $smalt_k ) if ( defined($smalt_k) ); $self->smalt_s( $smalt_s ) if ( defined($smalt_s) ); $self->smalt_y( $smalt_y ) if ( defined($smalt_y) ); @@ -76,6 +74,7 @@ reference => $self->reference, refname => $self->refname, outfile => $self->outfile, + smalt => $self->smalt, smalt_k => $self->smalt_k, smalt_s => $self->smalt_s, smalt_y => $self->smalt_y, @@ -87,8 +86,8 @@ sub usage_text { print <meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::RunMapping - Perform mapping + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a reference genome and indexes it. +Maps given fastq files to ref. + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisAnalysis.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,13 +1,7 @@ package Bio::Tradis::CommandLine::TradisAnalysis; - +$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.4.5'; # ABSTRACT: Perform full tradis analysis -=head1 SYNOPSIS - -Takes a fastq, reference and a tag and generates insertion -site plots for use in Artemis - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -18,7 +12,7 @@ has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 ); has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 ); -has 'tag' => ( is => 'rw', isa => 'Str', required => 0 ); +has 'tag' => ( is => 'rw', isa => 'Maybe[Str]', required => 0 ); has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 ); has 'tagdirection' => ( is => 'rw', isa => 'Str', required => 0, default => '3' ); @@ -26,6 +20,8 @@ has 'help' => ( is => 'rw', isa => 'Bool', required => 0 ); has 'mapping_score' => ( is => 'rw', isa => 'Int', required => 0, default => 30 ); +has 'min_seed_len' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); +has 'smalt' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 ); @@ -56,7 +52,7 @@ my ($self) = @_; my ( - $fastqfile, $tag, $td, $mismatch, $ref,$smalt_n, $essentiality, + $fastqfile, $tag, $td, $mismatch, $ref,$smalt_n, $essentiality, $min_seed_len, $smalt, $map_score, $smalt_k, $smalt_s, $smalt_y, $smalt_r, $help, $verbose,$samtools_exec ); @@ -68,14 +64,16 @@ 'mm|mismatch=i' => \$mismatch, 'r|reference=s' => \$ref, 'm|mapping_score=i' => \$map_score, + 'k|min_seed_len=i' => \$min_seed_len, + 's|smalt' => \$smalt, 'sk|smalt_k=i' => \$smalt_k, 'ss|smalt_s=i' => \$smalt_s, 'sy|smalt_y=f' => \$smalt_y, - 'n|smalt_n=i' => \$smalt_n, - 'sr|smalt_r=i' => \$smalt_r, + 'n|smalt_n=i' => \$smalt_n, + 'sr|smalt_r=i' => \$smalt_r, 'v|verbose' => \$verbose, 'samtools_exec=s' => \$samtools_exec, - 'e|essentiality' => \$essentiality, + 'e|essentiality' => \$essentiality, 'h|help' => \$help ); @@ -93,17 +91,22 @@ $self->mismatch($mismatch) if ( defined($mismatch) ); $self->reference( abs_path($ref) ) if ( defined($ref) ); $self->mapping_score($map_score) if ( defined($map_score) ); + $self->min_seed_len($min_seed_len) if ( defined($min_seed_len) ); + $self->smalt($smalt) if ( defined($smalt) ); $self->smalt_k($smalt_k) if ( defined($smalt_k) ); $self->smalt_s($smalt_s) if ( defined($smalt_s) ); $self->smalt_y($smalt_y) if ( defined($smalt_y) ); - $self->smalt_r($smalt_r) if ( defined($smalt_r) ); - $self->smalt_n($smalt_n) if ( defined($smalt_n) ); + $self->smalt_r($smalt_r) if ( defined($smalt_r) ); + $self->smalt_n($smalt_n) if ( defined($smalt_n) ); $self->help($help) if ( defined($help) ); $self->verbose($verbose) if ( defined($verbose)); $self->samtools_exec($samtools_exec) if ( defined($samtools_exec) ); + + # print usage text if required parameters are not present - ( $fastqfile && $tag && $ref ) or die $self->usage_text; + ( $fastqfile ) or die "--fastqfile required/n" . $self->usage_text; + ( $ref ) or die "--reference required\n" . $self->usage_text; } sub run { @@ -149,11 +152,13 @@ mapping_score => $self->mapping_score, output_directory => $self->_output_directory, _stats_handle => $self->_stats_handle, + min_seed_len => $self->min_seed_len, + smalt => $self->smalt, smalt_k => $self->smalt_k, smalt_s => $self->smalt_s, smalt_y => $self->smalt_y, smalt_r => $self->smalt_r, - smalt_n => $self->smalt_n, + smalt_n => $self->smalt_n, verbose => $self->verbose, samtools_exec => $self->samtools_exec ); @@ -250,11 +255,13 @@ Options: -f : text file listing fastq files with tradis tags attached --t : tag to search for +-t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.) -r : reference genome in fasta format (.fa) -td : tag direction - 3 or 5 (optional. default = 3) -mm : number of mismatches allowed when matching tag (optional. default = 0) -m : mapping quality cutoff score (optional. default = 30) +-k : custom k-mer value (min seed length) (optional) +--smalt : use smalt rather than bwa as the mapper --smalt_k : custom k-mer value for SMALT mapping (optional) --smalt_s : custom step size for SMALT mapping (optional) --smalt_y : custom y parameter for SMALT (optional. default = 0.96) @@ -269,3 +276,36 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::TradisAnalysis - Perform full tradis analysis + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a fastq, reference and a tag and generates insertion +site plots for use in Artemis + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/TradisBam.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisBam.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/CommandLine/TradisBam.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/CommandLine/TradisBam.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,13 +1,7 @@ package Bio::Tradis::CommandLine::TradisBam; - +$Bio::Tradis::CommandLine::TradisBam::VERSION = '1.4.5'; # ABSTRACT: Adds tags to sequences if tags are present -=head1 SYNOPSIS - -Checks for tradis tags in the BAM and outputs processed TraDIS BAM file -with tags attached - -=cut use Moose; use Getopt::Long qw(GetOptionsFromArray); @@ -100,3 +94,36 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::CommandLine::TradisBam - Adds tags to sequences if tags are present + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Checks for tradis tags in the BAM and outputs processed TraDIS BAM file +with tags attached + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/DetectTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/DetectTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/DetectTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/DetectTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,30 +1,7 @@ package Bio::Tradis::DetectTags; - +$Bio::Tradis::DetectTags::VERSION = '1.4.5'; # ABSTRACT: Detect tr tags in BAM file -=head1 NAME - -Bio::Tradis::DetectTags - -=head1 SYNOPSIS - -Detects presence of tr/tq tags in BAM files from Tradis analyses - use Bio::Tradis::DetectTags; - - my $pipeline = Bio::Tradis::DetectTags->new(bamfile => 'abc'); - $pipeline->tags_present(); - -=head1 PARAMETERS - -=head2 Required - -C - path to/name of file to check - -=head1 METHODS - -C - returns true if TraDIS tags are detected in C - -=cut use Moose; use Bio::Tradis::Parser::Bam @@ -52,3 +29,53 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::DetectTags - Detect tr tags in BAM file + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Detects presence of tr/tq tags in BAM files from Tradis analyses + use Bio::Tradis::DetectTags; + + my $pipeline = Bio::Tradis::DetectTags->new(bamfile => 'abc'); + $pipeline->tags_present(); + +=head1 NAME + +Bio::Tradis::DetectTags + +=head1 PARAMETERS + +=head2 Required + +C - path to/name of file to check + +=head1 METHODS + +C - returns true if TraDIS tags are detected in C + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Exception.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Exception.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Exception.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Exception.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,11 +1,6 @@ package Bio::Tradis::Exception; # ABSTRACT: Exceptions for input data - -=head1 SYNOPSIS - -Exceptions for input data - -=cut +$Bio::Tradis::Exception::VERSION = '1.4.5'; use Exception::Class ( @@ -14,3 +9,35 @@ ); 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Exception - Exceptions for input data + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Exceptions for input data + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/FilterTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/FilterTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/FilterTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/FilterTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,45 +1,7 @@ package Bio::Tradis::FilterTags; - +$Bio::Tradis::FilterTags::VERSION = '1.4.5'; # ABSTRACT: Filter tags in a fastq file -=head1 SYNOPSIS - -Reads in a fastq file with tradis tags already attached to the start of the sequence -Filters reads that contain the provided tag -Outputs a file *.tag.fastq unless an alternative outfile name is specified - - use Bio::Tradis::FilterTags; - - my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc'); - $pipeline->filter_tags(); - -=head1 PARAMETERS - -=head2 Required - -=over - -=item * C - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion. - -=item * C - TraDIS tag to match - -=back - -=head2 Optional - -=over - -=item * C - number of mismatches to allow when matching the tag. Default = 0 - -=item * C - output file name. Defaults to C for an input file named C - -=back - -=head1 METHODS - -C - outputs all reads containing the provided tag to C - -=cut use Moose; use Bio::Tradis::Parser::Fastq; @@ -160,3 +122,68 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::FilterTags - Filter tags in a fastq file + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Reads in a fastq file with tradis tags already attached to the start of the sequence +Filters reads that contain the provided tag +Outputs a file *.tag.fastq unless an alternative outfile name is specified + + use Bio::Tradis::FilterTags; + + my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc'); + $pipeline->filter_tags(); + +=head1 PARAMETERS + +=head2 Required + +=over + +=item * C - path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion. + +=item * C - TraDIS tag to match + +=back + +=head2 Optional + +=over + +=item * C - number of mismatches to allow when matching the tag. Default = 0 + +=item * C - output file name. Defaults to C for an input file named C + +=back + +=head1 METHODS + +C - outputs all reads containing the provided tag to C + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Map.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Map.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Map.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,67 +1,7 @@ package Bio::Tradis::Map; - +$Bio::Tradis::Map::VERSION = '1.4.5'; # ABSTRACT: Perform mapping -=head1 SYNOPSIS - -Takes a reference genome and indexes it. -Maps given fastq files to ref. - - use Bio::Tradis::Map; - - my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc'); - $pipeline->index_ref(); - $pipeline->do_mapping(); - -=head1 PARAMETERS - -=head2 Required - -=over - -=item * C - path to/name of file containing reads to map to the reference - -=item * C - path to/name of reference genome in fasta format (.fa) - -=back - -=head2 Optional - -=over - -=item * C - name to assign to the reference index files. Default = ref.index - -=item * C - name to assign to the mapped SAM file. Default = mapped.sam - -=back - -=head1 METHODS - -=over - -=item * C - create index files of the reference genome. These are required - for the mapping step. Only skip this step if index files already - exist. -k and -s options for referencing are calculated based - on the length of the reads being mapped as per table: - -=begin html - - - - - - -
Read lengthks
<70134
>70 and <100136
>100206
- -=end html - -=item * C - map C to C. Options used for mapping are: C<-r -1 -x -y 0.96> - -=back - -For more information on the mapping and indexing options discussed here, see the L - -=cut use Moose; use Bio::Tradis::Parser::Fastq; @@ -72,6 +12,8 @@ ( is => 'rw', isa => 'Str', required => 0, default => 'ref.index' ); has 'outfile' => ( is => 'rw', isa => 'Str', required => 0, default => 'mapped.sam' ); +has 'min_seed_len' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); +has 'smalt' => ( is => 'rw', isa => 'Bool', required => 0, default => 0 ); has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 ); @@ -83,23 +25,32 @@ my $ref = $self->reference; my $refname = $self->refname; - # Calculate index parameters + my $cmd = ""; + if ($self->smalt) { + # Calculate index parameters + my $read_len = $self->_calculate_read_len(); + my ( $k, $s ) = $self->_calculate_index_parameters($read_len); + $cmd = "smalt index -k $k -s $s $refname $ref > /dev/null 2>&1"; + } else { + $cmd = "bwa index $ref > /dev/null 2>&1" + } + system($cmd); + return $cmd; +} + +sub _calculate_read_len { + my ($self) = @_; my $pars = Bio::Tradis::Parser::Fastq->new( file => $self->fastqfile ); $pars->next_read; my @read = $pars->read_info; - my $read_len = length($read[1]); - my ( $k, $s ) = $self->_calculate_index_parameters($read_len); - - my $cmd = "smalt index -k $k -s $s $refname $ref > /dev/null 2>&1"; - system($cmd); - return $cmd; + return length($read[1]); } sub _calculate_index_parameters { my ($self, $read_len) = @_; my ( $k, $s ); - - if( defined $self->smalt_k ){ $k = $self->smalt_k; } + + if ( defined $self->smalt_k ){ $k = $self->smalt_k; } else{ $k = $self->_smalt_k_default($read_len); } if( defined $self->smalt_s ){ $s = $self->smalt_s; } @@ -108,6 +59,12 @@ return ( $k, $s ); } +sub _min_seed_len_default { + my ($self, $read_len) = @_; + if($read_len < 100){ return 13; } + else{ return 19; } +} + sub _smalt_k_default { my ($self, $read_len) = @_; if($read_len < 100){ return 13; } @@ -124,20 +81,114 @@ sub do_mapping { my ($self) = @_; my $fqfile = $self->fastqfile; + my $ref = $self->reference; my $refname = $self->refname; my $outfile = $self->outfile; my $y = $self->smalt_y; my $r = $self->smalt_r; - my $n = $self->smalt_n; + my $n = $self->smalt_n; - my $smalt = "smalt map -n $n -x -r $r -y $y $refname $fqfile 1> $outfile 2> smalt.stderr"; + my $align = ""; + if ($self->smalt) { + $align = "smalt map -n $n -x -r $r -y $y $refname $fqfile 1> $outfile 2> align.stderr"; + } else { + my $read_len = $self->_calculate_read_len(); + my $k = ( defined $self->min_seed_len ) ? + $self->min_seed_len : + $self->_min_seed_len_default($read_len); + + $align = "bwa mem -k $k -t $n $ref $fqfile 1> $outfile 2> align.stderr"; + } - system($smalt); - unlink('smalt.stderr'); + system($align); + unlink('align.stderr'); - return $smalt; + return $align; } __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Map - Perform mapping + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a reference genome and indexes it. +Maps given fastq files to ref. + + use Bio::Tradis::Map; + + my $pipeline = Bio::Tradis::Map->new(fastqfile => 'abc', reference => 'abc'); + $pipeline->index_ref(); + $pipeline->do_mapping(); + +=head1 PARAMETERS + +=head2 Required + +=over + +=item * C - path to/name of file containing reads to map to the reference + +=item * C - path to/name of reference genome in fasta format (.fa) + +=back + +=head2 Optional + +=over + +=item * C - name to assign to the reference index files. Default = ref.index + +=item * C - name to assign to the mapped SAM file. Default = mapped.sam + +=back + +=head1 METHODS + +=over + +=item * C - create index files of the reference genome. These are required + for the mapping step. Only skip this step if index files already + exist. -k and -s options for referencing are calculated based + on the length of the reads being mapped as per table: + +=for html + + + + +
Read lengthks
<70134
>70 and <100136
>100206
+ +=item * C - map C to C. Options used for mapping are: C<-r -1 -x -y 0.96> + +=back + +For more information on the mapping and indexing options discussed here, see the L + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Bam.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Bam.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Bam.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Bam.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,21 +1,7 @@ package Bio::Tradis::Parser::Bam; - +$Bio::Tradis::Parser::Bam::VERSION = '1.4.5'; # ABSTRACT: Very basic BAM parser. Limited functionality. -=head1 SYNOPSIS - -Parses BAM files and gives access to basic info in them. - - use Bio::Tradis::Parser::Bam; - - my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc'); - $pipeline->read_info; - $pipeline->next_read; - $pipeline->seq_info; - $pipeline->is_mapped; - $pipeline->is_reverse; - -=cut use Moose; @@ -82,10 +68,6 @@ ### Public methods ### -=seq_info -Reads BAM header and returns a hash (keys are sequence ids, values are hash -refs with keys as tags (like LN and M5)) -=cut sub seq_info { my ($self) = @_; @@ -111,9 +93,6 @@ return %all_seq_info; } -=next_read -Moves _currentread to the next entry in the BAM. Returns 0 if EOF. -=cut sub next_read { my ($self) = @_; @@ -135,33 +114,12 @@ close $self->_bam_handle; } -=read_info -Returns info from _currentread = hash reference with field name as key. -Standard fields are named as per the SAM format specification: -1 : QNAME -2 : FLAG -3 : RNAME -4 : POS -5 : MAPQ -6 : CIGAR -7 : RNEXT -8 : PNEXT -9 : TLEN -10 : SEQ -11 : QUAL -Additional fields will use their tag names. -Complete line is returned with key READ -=cut sub read_info { my ($self) = @_; return $self->_currentread; } -=is_mapped -Parses the flag for the current read and determines if mapped. -Returns 0 or 1. -=cut sub is_mapped { my ($self) = @_; @@ -173,10 +131,6 @@ return $resl; } -=is_reverse -Parses the flag for the current read and determines if reverse -complemented. Returns 0 or 1. -=cut sub is_reverse { my ($self) = @_; @@ -190,3 +144,76 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Parser::Bam - Very basic BAM parser. Limited functionality. + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Parses BAM files and gives access to basic info in them. + + use Bio::Tradis::Parser::Bam; + + my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc'); + $pipeline->read_info; + $pipeline->next_read; + $pipeline->seq_info; + $pipeline->is_mapped; + $pipeline->is_reverse; + +=seq_info +Reads BAM header and returns a hash (keys are sequence ids, values are hash +refs with keys as tags (like LN and M5)) + +=next_read +Moves _currentread to the next entry in the BAM. Returns 0 if EOF. + +=read_info +Returns info from _currentread = hash reference with field name as key. +Standard fields are named as per the SAM format specification: +1 : QNAME +2 : FLAG +3 : RNAME +4 : POS +5 : MAPQ +6 : CIGAR +7 : RNEXT +8 : PNEXT +9 : TLEN +10 : SEQ +11 : QUAL +Additional fields will use their tag names. +Complete line is returned with key READ + +=is_mapped +Parses the flag for the current read and determines if mapped. +Returns 0 or 1. + +=is_reverse +Parses the flag for the current read and determines if reverse +complemented. Returns 0 or 1. + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Cigar.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Cigar.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Cigar.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Cigar.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,18 +1,7 @@ package Bio::Tradis::Parser::Cigar; - +$Bio::Tradis::Parser::Cigar::VERSION = '1.4.5'; # ABSTRACT: Take in a cigar string and output start and end relative to the reference sequence -=head1 SYNOPSIS - -Take in a cigar string and output start and end relative to the reference sequence - - use Bio::Tradis::Parser::Cigar; - - my $cigar = Bio::Tradis::Parser::Cigar->new(coordinate => 123, cigar => '10S90M'); - $cigar->start; - $cigar->end; - -=cut use Moose; @@ -69,3 +58,41 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Parser::Cigar - Take in a cigar string and output start and end relative to the reference sequence + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Take in a cigar string and output start and end relative to the reference sequence + + use Bio::Tradis::Parser::Cigar; + + my $cigar = Bio::Tradis::Parser::Cigar->new(coordinate => 123, cigar => '10S90M'); + $cigar->start; + $cigar->end; + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Fastq.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Fastq.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Parser/Fastq.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Parser/Fastq.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,18 +1,7 @@ package Bio::Tradis::Parser::Fastq; - +$Bio::Tradis::Parser::Fastq::VERSION = '1.4.5'; # ABSTRACT: Basic FastQ parser. -=head1 SYNOPSIS - -Parses fastq files. - - use Bio::Tradis::Parser::Fastq; - - my $pipeline = Bio::Tradis::Parser::Fastq->new(file => 'abc'); - $pipeline->next_read; - $pipeline->read_info; - -=cut use Moose; @@ -42,10 +31,6 @@ ### Public methods ### -=next_read -Moves to the next read. Returns 1 if read exists, returns 0 -if EOF -=cut sub next_read { my ($self) = @_; @@ -61,12 +46,6 @@ } } -=read_info -Returns an array of info for the read in an array. -0 = id -1 = sequence -2 = quality string -=cut sub read_info { my ($self) = @_; my $fqh = $self->_fastq_handle; @@ -99,3 +78,51 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Parser::Fastq - Basic FastQ parser. + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Parses fastq files. + + use Bio::Tradis::Parser::Fastq; + + my $pipeline = Bio::Tradis::Parser::Fastq->new(file => 'abc'); + $pipeline->next_read; + $pipeline->read_info; + +=next_read +Moves to the next read. Returns 1 if read exists, returns 0 +if EOF + +=read_info +Returns an array of info for the read in an array. +0 = id +1 = sequence +2 = quality string + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/RemoveTags.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RemoveTags.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/RemoveTags.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RemoveTags.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,45 +1,7 @@ package Bio::Tradis::RemoveTags; - +$Bio::Tradis::RemoveTags::VERSION = '1.4.5'; # ABSTRACT: Remove tags from seqs a fastq file -=head1 SYNOPSIS - -Reads in a fastq file with tradis tags already attached to the start of the sequence -Removes tags from the sequence and quality strings -Outputs a file *.rmtag.fastq unless an out file is specified - - use Bio::Tradis::RemoveTags; - - my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc'); - $pipeline->remove_tags(); - -=head1 PARAMETERS - -=head2 Required - -=over - -=item * C - path to/name of file to filter - -=item * C - TraDIS tag to remove - -=back - -=head2 Optional - -=over - -=item * C - number of mismatches to allow when removing the tag. Default = 0 - -=item * C - defaults to C for and input file named C - -=back - -=head1 METHODS - -C - output all reads with the tags removed to C - -=cut use Moose; use Bio::Tradis::Parser::Fastq; @@ -120,3 +82,68 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Reads in a fastq file with tradis tags already attached to the start of the sequence +Removes tags from the sequence and quality strings +Outputs a file *.rmtag.fastq unless an out file is specified + + use Bio::Tradis::RemoveTags; + + my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc'); + $pipeline->remove_tags(); + +=head1 PARAMETERS + +=head2 Required + +=over + +=item * C - path to/name of file to filter + +=item * C - TraDIS tag to remove + +=back + +=head2 Optional + +=over + +=item * C - number of mismatches to allow when removing the tag. Default = 0 + +=item * C - defaults to C for and input file named C + +=back + +=head1 METHODS + +C - output all reads with the tags removed to C + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/RunTradis.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/RunTradis.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/RunTradis.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,57 +1,7 @@ package Bio::Tradis::RunTradis; - +$Bio::Tradis::RunTradis::VERSION = '1.4.5'; # ABSTRACT: Perform all steps required for a tradis analysis -=head1 SYNOPSIS - -Takes a fastq file with tags already attached, filters the tags matching user input, -removes the tags, maps to a reference (.fa) and generates insertion site plots for use in -Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis. - - use Bio::Tradis::RunTradis; - - my $pipeline = Bio::Tradis::RunTradis->new( - fastqfile => 'abc', - reference => 'abc', - tag => 'abc', - tagdirection => '5'|'3' - ); - $pipeline->run_tradis(); - -=head1 PARAMETERS - -=head2 Required - -=over - -=item * C - file containing a list of fastqs (gzipped or raw) to run the - complete analysis on. This includes all (including - intermediary format conversion and sorting) steps starting from - filtering. - -=item * C - TraDIS tag to filter and then remove - -=item * C - path to/name of reference genome in fasta format (.fa) - -=back - -=head2 Optional - -=over - -=item * C - number of mismatches to allow when filtering/removing the tag. Default = 0 - -=item * C - direction of the tag, 5' or 3'. Default = 3 - -=item * C - cutoff value for mapping score when creating insertion site plots. Default = 30 - -=back - -=head1 METHODS - -C - run complete analysis with given parameters - -=cut use Cwd; use Moose; @@ -68,7 +18,7 @@ has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 1 ); has '_unzipped_fastq' => ( is => 'rw', isa => 'Str', lazy => 1, builder => '_build__unzipped_fastq' ); -has 'tag' => ( is => 'ro', isa => 'Str', required => 1 ); +has 'tag' => ( is => 'ro', isa => 'Maybe[Str]', required => 0 ); has 'tagdirection' => ( is => 'ro', isa => 'Str', required => 1, default => '3' ); has 'mismatch' => ( is => 'rw', isa => 'Int', required => 1, default => 0 ); @@ -87,6 +37,8 @@ return $o; } ); +has 'min_seed_len' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); +has 'smalt' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 ); has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 ); @@ -209,20 +161,24 @@ print STDERR "::::::::::::::::::\n$fq\n::::::::::::::::::\n\n" if($self->verbose); - # Step 1: Filter tags that match user input tag - print STDERR "..........Step 1: Filter tags that match user input tag\n" if($self->verbose); - $self->_filter; - - print STDERR "..........Step 1.1: Check that at least one read started with the tag\n" if($self->verbose); - $self->_check_filter; - - # Step 2: Remove the tag from the sequence and quality strings - print STDERR -"..........Step 2: Remove the tag from the sequence and quality strings\n" if($self->verbose); - $self->_remove; + if (defined($self->tag)) { + # Step 1: Filter tags that match user input tag + print STDERR "..........Step 1: Filter tags that match user input tag\n" if($self->verbose); + $self->_filter; + + print STDERR "..........Step 1.1: Check that at least one read started with the tag\n" if($self->verbose); + $self->_check_filter; + + # Step 2: Remove the tag from the sequence and quality strings + print STDERR "..........Step 2: Remove the tag from the sequence and quality strings\n" if($self->verbose); + $self->_remove; + } else { + print STDERR "..........Tagless mode selected skipping steps 1 and 2\n" if($self->verbose); + } # Step 3: Map file to reference - print STDERR "..........Step 3: Map file to reference\n" if($self->verbose); + my $mapper = $self->smalt ? "smalt" : "bwa"; + print STDERR "..........Step 3: Map file to reference using $mapper\n" if($self->verbose); $self->_map; # Step 4: Convert output from SAM to BAM, sort and index @@ -317,17 +273,20 @@ my $temporary_directory = $self->_temp_directory; my $ref = $self->reference; + my $fqfile = !defined($self->tag) ? $self->_unzipped_fastq : "$temporary_directory/tags_removed.fastq"; my $mapping = Bio::Tradis::Map->new( - fastqfile => "$temporary_directory/tags_removed.fastq", + fastqfile => $fqfile, reference => "$ref", refname => "$temporary_directory/ref.index", outfile => "$temporary_directory/mapped.sam", + min_seed_len => $self->min_seed_len, smalt_k => $self->smalt_k, smalt_s => $self->smalt_s, smalt_y => $self->smalt_y, smalt_r => $self->smalt_r, - smalt_n => $self->smalt_n + smalt_n => $self->smalt_n, + smalt => $self->smalt ); $mapping->index_ref; $mapping->do_mapping; @@ -425,9 +384,11 @@ $stats .= "$total_reads,"; # Matching reads - my $matching = - `wc $temporary_directory/filter.fastq | awk '{print \$1/4}'`; - chomp($matching); + my $matching = $total_reads; + if (defined($self->tag)) { + $matching = `wc $temporary_directory/filter.fastq | awk '{print \$1/4}' `; + chomp($matching); + } $stats .= "$matching,"; $stats .= ( $matching / $total_reads ) * 100 . ","; @@ -509,3 +470,80 @@ __PACKAGE__->meta->make_immutable; no Moose; 1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Takes a fastq file with tags already attached, filters the tags matching user input, +removes the tags, maps to a reference (.fa) and generates insertion site plots for use in +Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis. + + use Bio::Tradis::RunTradis; + + my $pipeline = Bio::Tradis::RunTradis->new( + fastqfile => 'abc', + reference => 'abc', + tag => 'abc', + tagdirection => '5'|'3' + ); + $pipeline->run_tradis(); + +=head1 PARAMETERS + +=head2 Required + +=over + +=item * C - file containing a list of fastqs (gzipped or raw) to run the + complete analysis on. This includes all (including + intermediary format conversion and sorting) steps starting from + filtering. + +=item * C - path to/name of reference genome in fasta format (.fa) + +=back + +=head2 Optional + +=over + +=item * C - number of mismatches to allow when filtering/removing the tag. Default = 0 + +=item * C - direction of the tag, 5' or 3'. Default = 3 + +=item * C - cutoff value for mapping score when creating insertion site plots. Default = 30 + +=item * C - TraDIS tag to filter and then remove + +=back + +=head1 METHODS + +C - run complete analysis with given parameters + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Samtools.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/Samtools.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/Samtools.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,19 +1,7 @@ package Bio::Tradis::Samtools; - +$Bio::Tradis::Samtools::VERSION = '1.4.5'; # ABSTRACT: Change samtools syntax depending on version found -=head1 SYNOPSIS - -Change samtools syntax depending on version found - use Bio::Tradis::Samtools; - - my $obj = Bio::Tradis::Samtools->new( - exec => 'samtools' - ); - - $obj->run_sort(); - -=cut use Moose; use File::Spec; @@ -100,3 +88,41 @@ 1; +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::Samtools - Change samtools syntax depending on version found + +=head1 VERSION + +version 1.4.5 + +=head1 SYNOPSIS + +Change samtools syntax depending on version found + use Bio::Tradis::Samtools; + + my $obj = Bio::Tradis::Samtools->new( + exec => 'samtools' + ); + + $obj->run_sort(); + +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/TradisPlot.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/TradisPlot.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis/TradisPlot.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis/TradisPlot.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,7 +1,47 @@ package Bio::Tradis::TradisPlot; - +$Bio::Tradis::TradisPlot::VERSION = '1.4.5'; # ABSTRACT: Generate plots as part of a tradis analysis + +use Moose; +use Bio::Tradis::Analysis::InsertSite; + +has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 ); +has 'outfile' => + ( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' ); +has 'mapping_score' => + ( is => 'rw', isa => 'Int', required => 1, default => 30 ); + +sub plot { + my ($self) = @_; + + Bio::Tradis::Analysis::InsertSite->new( + filename => $self->mappedfile, + output_base_filename => $self->outfile, + mapping_score => $self->mapping_score + )->create_plots; + + return 1; +} + +__PACKAGE__->meta->make_immutable; +no Moose; +1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis + +=head1 VERSION + +version 1.4.5 + =head1 SYNOPSIS Generate insertion plots for Artemis from a mapped fastq file and a reference @@ -32,29 +72,16 @@ C - create insertion site plots for reads in `mappedfile`. This file will be readable by the L -=cut +=head1 AUTHOR -use Moose; -use Bio::Tradis::Analysis::InsertSite; +Carla Cummins -has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 ); -has 'outfile' => - ( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' ); -has 'mapping_score' => - ( is => 'rw', isa => 'Int', required => 1, default => 30 ); +=head1 COPYRIGHT AND LICENSE -sub plot { - my ($self) = @_; +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. - Bio::Tradis::Analysis::InsertSite->new( - filename => $self->mappedfile, - output_base_filename => $self->outfile, - mapping_score => $self->mapping_score - )->create_plots; +This is free software, licensed under: - return 1; -} + The GNU General Public License, Version 3, June 2007 -__PACKAGE__->meta->make_immutable; -no Moose; -1; +=cut diff -Nru bio-tradis-1.4.1+dfsg/lib/Bio/Tradis.pm bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis.pm --- bio-tradis-1.4.1+dfsg/lib/Bio/Tradis.pm 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/lib/Bio/Tradis.pm 2019-12-04 14:40:22.000000000 +0000 @@ -1,9 +1,25 @@ use strict; use warnings; package Bio::Tradis; - +$Bio::Tradis::VERSION = '1.4.5'; # ABSTRACT: Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308 +1; + +__END__ + +=pod + +=encoding UTF-8 + +=head1 NAME + +Bio::Tradis - Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308 + +=head1 VERSION + +version 1.4.5 + =head1 SYNOPSIS Bio-Tradis provides functionality to: @@ -26,6 +42,16 @@ Most of these functions are available as standalone scripts or as perl modules. +=head1 AUTHOR + +Carla Cummins + +=head1 COPYRIGHT AND LICENSE + +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 =cut -1; diff -Nru bio-tradis-1.4.1+dfsg/LICENSE bio-tradis-1.4.5+dfsg2/LICENSE --- bio-tradis-1.4.1+dfsg/LICENSE 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/LICENSE 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,680 @@ +This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + +This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + 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 . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff -Nru bio-tradis-1.4.1+dfsg/Makefile.PL bio-tradis-1.4.5+dfsg2/Makefile.PL --- bio-tradis-1.4.1+dfsg/Makefile.PL 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/Makefile.PL 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,100 @@ +# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.012. +use strict; +use warnings; + + + +use ExtUtils::MakeMaker; + +my %WriteMakefileArgs = ( + "ABSTRACT" => "Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308", + "AUTHOR" => "Carla Cummins ", + "CONFIGURE_REQUIRES" => { + "ExtUtils::MakeMaker" => 0 + }, + "DISTNAME" => "Bio-Tradis", + "EXE_FILES" => [ + "bin/add_tradis_tags", + "bin/bacteria_tradis", + "bin/check_tradis_tags", + "bin/combine_tradis_plots", + "bin/filter_tradis_tags", + "bin/remove_tradis_tags", + "bin/tradis_comparison.R", + "bin/tradis_essentiality.R", + "bin/tradis_gene_insert_sites", + "bin/tradis_merge_plots", + "bin/tradis_plot" + ], + "LICENSE" => "gpl", + "NAME" => "Bio::Tradis", + "PREREQ_PM" => { + "Bio::Seq" => 0, + "Bio::SeqIO" => 0, + "Cwd" => 0, + "Data::Dumper" => 0, + "Exception::Class" => 0, + "File::Basename" => 0, + "File::Path" => 0, + "File::Spec" => 0, + "File::Temp" => 0, + "FindBin" => 0, + "Getopt::Long" => 0, + "Moose" => 0, + "Text::CSV" => 0, + "Try::Tiny" => 0, + "strict" => 0, + "warnings" => 0 + }, + "TEST_REQUIRES" => { + "Env::Path" => "0.18", + "ExtUtils::MakeMaker" => 0, + "File::Spec" => 0, + "Test::Exception" => 0, + "Test::Files" => 0, + "Test::More" => 0, + "Test::Most" => 0 + }, + "VERSION" => "1.4.5", + "test" => { + "TESTS" => "t/*.t t/Bio/Tradis/*.t t/Bio/Tradis/Analysis/*.t t/Bio/Tradis/CommandLine/*.t t/Bio/Tradis/Parser/*.t" + } +); + + +my %FallbackPrereqs = ( + "Bio::Seq" => 0, + "Bio::SeqIO" => 0, + "Cwd" => 0, + "Data::Dumper" => 0, + "Env::Path" => "0.18", + "Exception::Class" => 0, + "ExtUtils::MakeMaker" => 0, + "File::Basename" => 0, + "File::Path" => 0, + "File::Spec" => 0, + "File::Temp" => 0, + "FindBin" => 0, + "Getopt::Long" => 0, + "Moose" => 0, + "Test::Exception" => 0, + "Test::Files" => 0, + "Test::More" => 0, + "Test::Most" => 0, + "Text::CSV" => 0, + "Try::Tiny" => 0, + "strict" => 0, + "warnings" => 0 +); + + +unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) { + delete $WriteMakefileArgs{TEST_REQUIRES}; + delete $WriteMakefileArgs{BUILD_REQUIRES}; + $WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs; +} + +delete $WriteMakefileArgs{CONFIGURE_REQUIRES} + unless eval { ExtUtils::MakeMaker->VERSION(6.52) }; + +WriteMakefile(%WriteMakefileArgs); diff -Nru bio-tradis-1.4.1+dfsg/MANIFEST bio-tradis-1.4.5+dfsg2/MANIFEST --- bio-tradis-1.4.1+dfsg/MANIFEST 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/MANIFEST 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,194 @@ +# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.012. +AUTHORS +BioTraDISTutorial.pdf +CHANGELOG.md +Dockerfile +LICENSE +MANIFEST +META.json +META.yml +Makefile.PL +README +README.md +_config.yml +bcinstall.log +bin/add_tradis_tags +bin/bacteria_tradis +bin/check_tradis_tags +bin/combine_tradis_plots +bin/filter_tradis_tags +bin/remove_tradis_tags +bin/tradis_comparison.R +bin/tradis_essentiality.R +bin/tradis_gene_insert_sites +bin/tradis_merge_plots +bin/tradis_plot +build/bwa-0.7.17.tbz +build/samtools-1.3.tbz +build/smalt-0.7.6.tgz +build/tabix-master.tgz +dist.ini +install_dependencies.sh +lib/Bio/Tradis.pm +lib/Bio/Tradis/AddTagsToSeq.pm +lib/Bio/Tradis/Analysis/Exceptions.pm +lib/Bio/Tradis/Analysis/InsertSite.pm +lib/Bio/Tradis/CombinePlots.pm +lib/Bio/Tradis/CommandLine/AddTags.pm +lib/Bio/Tradis/CommandLine/CheckTags.pm +lib/Bio/Tradis/CommandLine/FilterFastqTags.pm +lib/Bio/Tradis/CommandLine/PlotCombine.pm +lib/Bio/Tradis/CommandLine/PlotTradis.pm +lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm +lib/Bio/Tradis/CommandLine/RunMapping.pm +lib/Bio/Tradis/CommandLine/TradisAnalysis.pm +lib/Bio/Tradis/CommandLine/TradisBam.pm +lib/Bio/Tradis/DetectTags.pm +lib/Bio/Tradis/Exception.pm +lib/Bio/Tradis/FilterTags.pm +lib/Bio/Tradis/Map.pm +lib/Bio/Tradis/Parser/Bam.pm +lib/Bio/Tradis/Parser/Cigar.pm +lib/Bio/Tradis/Parser/Fastq.pm +lib/Bio/Tradis/RemoveTags.pm +lib/Bio/Tradis/RunTradis.pm +lib/Bio/Tradis/Samtools.pm +lib/Bio/Tradis/TradisPlot.pm +recipes/Tradis_SR_RR_12dark_42r1_rehyb12_index8.xml +recipes/Tradis_adapter_primers.xlsx +recipes/Transposon10/Chemistry/Chemistry.xml +recipes/Transposon10/Exposures/Sony.xml +recipes/Transposon10/Exposures/SonyV2.xml +recipes/Transposon10/Protocol/1Read1Index.xml +recipes/Transposon10/Protocol/1Read2Index.xml +recipes/Transposon10/Protocol/2Read1Index.xml +recipes/Transposon10/Protocol/2Read2Index.xml +recipes/Transposon10/Reads/Reads.xml +recipes/Transposon10/Reagents/MaintenanceWash.xml +recipes/Transposon10/Reagents/PostRunWash.xml +recipes/Transposon10/Reagents/Sequencing.xml +recipes/Transposon10/Wash/LineWash.xml +recipes/Transposon10/Wash/MaintenanceWash.xml +recipes/Transposon10/Wash/PostRunWash.xml +recipes/Transposon10/Wash/PostRunWashOriginal.xml +recipes/Transposon10/Wash/StandbyWash.xml +recipes/Transposon12/Chemistry/Chemistry.xml +recipes/Transposon12/Exposures/Sony.xml +recipes/Transposon12/Exposures/SonyV2.xml +recipes/Transposon12/Protocol/1Read1Index.xml +recipes/Transposon12/Protocol/1Read2Index.xml +recipes/Transposon12/Protocol/2Read1Index.xml +recipes/Transposon12/Protocol/2Read2Index.xml +recipes/Transposon12/Reads/Reads.xml +recipes/Transposon12/Reagents/MaintenanceWash.xml +recipes/Transposon12/Reagents/PostRunWash.xml +recipes/Transposon12/Reagents/Sequencing.xml +recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx +recipes/Transposon12/Wash/LineWash.xml +recipes/Transposon12/Wash/MaintenanceWash.xml +recipes/Transposon12/Wash/PostRunWash.xml +recipes/Transposon12/Wash/PostRunWashOriginal.xml +recipes/Transposon12/Wash/StandbyWash.xml +software_license +source_path +t/00-report-prereqs.dd +t/00-report-prereqs.t +t/Bio/Tradis/AddTagsToSeq.t +t/Bio/Tradis/Analysis/InsertSite.t +t/Bio/Tradis/CombinePlots.t +t/Bio/Tradis/CommandLine/TradisAnalysis.t +t/Bio/Tradis/DetectTags.t +t/Bio/Tradis/FilterTags.t +t/Bio/Tradis/Map.t +t/Bio/Tradis/Parser/Bam.t +t/Bio/Tradis/Parser/Cigar.t +t/Bio/Tradis/Parser/Fastq.t +t/Bio/Tradis/RemoveTags.t +t/Bio/Tradis/RunTradisBWA.t +t/Bio/Tradis/RunTradisSmalt.t +t/Bio/Tradis/RunTradisTaglessBwa.t +t/Bio/Tradis/RunTradisTaglessSmalt.t +t/Bio/Tradis/TradisPlot.t +t/data/AddTags/expected_tradis.bam +t/data/AddTags/expected_tradis.cram +t/data/AddTags/sample_sm_no_tr.bam +t/data/AddTags/sample_sm_tr.bam +t/data/AddTags/sample_sm_tr.cram +t/data/CombinePlots/comb_expected.stats +t/data/CombinePlots/comb_sample.txt +t/data/CombinePlots/first.expected.plot +t/data/CombinePlots/sample1.sm.plot.gz +t/data/CombinePlots/sample2.sm.plot.gz +t/data/CombinePlots/second.expected.plot +t/data/CombinePlots/tabix_sorted.insert_site_plot.gz +t/data/CombinePlots/tabix_sorted.insert_site_plot.gz.tbi +t/data/CombinePlots/test1.plot +t/data/CombinePlots/test2.plot +t/data/CombinePlots/test3.plot +t/data/CombinePlots/test4.plot +t/data/CombinePlots/zip_comb_exp.plot +t/data/CombinePlots/zip_comb_exp.stats +t/data/CombinePlots/zip_comb_list.txt +t/data/CommandLine/fastq.list +t/data/CommandLine/test_1.fastq +t/data/CommandLine/test_2.fastq +t/data/DetectTags/AE004091.fasta +t/data/DetectTags/AE004091.fasta.fai +t/data/DetectTags/sample_sm_no_tr.bam +t/data/DetectTags/sample_sm_tr.bam +t/data/DetectTags/sample_sm_tr.cram +t/data/FilterTags/expected.1mm.caa.fastq +t/data/FilterTags/expected.caa.fastq +t/data/FilterTags/expected.tna.fastq +t/data/FilterTags/sample.fastq +t/data/FilterTags/sample.fastq.gz +t/data/InsertSite/2_reads.bam +t/data/InsertSite/small_multi_sequence.bam +t/data/Map/expected.bwa.mapped +t/data/Map/expected.smalt.mapped +t/data/Map/smallref.fa +t/data/Map/test.fastq +t/data/Parsers/test.bam +t/data/Parsers/test.fastq +t/data/RemoveTags/expected.rm.1mm.caa.fastq +t/data/RemoveTags/expected.rm.caa.fastq +t/data/RemoveTags/expected.rm.tna.fastq +t/data/RemoveTags/sample.caa.fastq +t/data/RemoveTags/sample.tna.fastq +t/data/RunTradisBWA/expected.1mm.plot.gz +t/data/RunTradisBWA/expected.plot.gz +t/data/RunTradisBWA/filelist.txt +t/data/RunTradisBWA/filtered.fastq +t/data/RunTradisBWA/mapped.sam +t/data/RunTradisBWA/notags.fastq +t/data/RunTradisBWA/smallref.fa +t/data/RunTradisBWA/test.tagged.fastq +t/data/RunTradisBWA/test.tagged.fastq.gz +t/data/RunTradisBWA/test2.tagged.fastq +t/data/RunTradisBWA/test2.tagged.fastq.gz +t/data/RunTradisSmalt/expected.1mm.plot.gz +t/data/RunTradisSmalt/expected.plot.gz +t/data/RunTradisSmalt/filelist.txt +t/data/RunTradisSmalt/filtered.fastq +t/data/RunTradisSmalt/mapped.sam +t/data/RunTradisSmalt/notags.fastq +t/data/RunTradisSmalt/smallref.fa +t/data/RunTradisSmalt/test.tagged.fastq +t/data/RunTradisSmalt/test.tagged.fastq.gz +t/data/RunTradisSmalt/test2.tagged.fastq +t/data/RunTradisSmalt/test2.tagged.fastq.gz +t/data/RunTradisTaglessBWA/expected.plot.gz +t/data/RunTradisTaglessBWA/filelist.txt +t/data/RunTradisTaglessBWA/mapped.sam +t/data/RunTradisTaglessBWA/notags.fastq +t/data/RunTradisTaglessBWA/smallref.fa +t/data/RunTradisTaglessSmalt/expected.plot.gz +t/data/RunTradisTaglessSmalt/mapped.sam +t/data/RunTradisTaglessSmalt/notags.fastq +t/data/RunTradisTaglessSmalt/smallref.fa +t/data/TradisPlot/expected.plot.gz +t/data/TradisPlot/sample.fastq +t/data/TradisPlot/test.mapped.bam +t/requires_external.t +xt/author/00-compile.t +xt/author/pod-syntax.t diff -Nru bio-tradis-1.4.1+dfsg/META.json bio-tradis-1.4.5+dfsg2/META.json --- bio-tradis-1.4.1+dfsg/META.json 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/META.json 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,654 @@ +{ + "abstract" : "Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308", + "author" : [ + "Carla Cummins " + ], + "dynamic_config" : 0, + "generated_by" : "Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010", + "license" : [ + "gpl_3" + ], + "meta-spec" : { + "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec", + "version" : 2 + }, + "name" : "Bio-Tradis", + "no_index" : { + "directory" : [ + "eg", + "examples", + "inc", + "share", + "t", + "xt" + ] + }, + "prereqs" : { + "configure" : { + "requires" : { + "ExtUtils::MakeMaker" : "0" + } + }, + "develop" : { + "requires" : { + "File::Spec" : "0", + "IO::Handle" : "0", + "IPC::Open3" : "0", + "Test::More" : "0", + "Test::Pod" : "1.41", + "perl" : "5.006" + } + }, + "runtime" : { + "requires" : { + "Bio::Seq" : "0", + "Bio::SeqIO" : "0", + "Cwd" : "0", + "Data::Dumper" : "0", + "Exception::Class" : "0", + "File::Basename" : "0", + "File::Path" : "0", + "File::Spec" : "0", + "File::Temp" : "0", + "FindBin" : "0", + "Getopt::Long" : "0", + "Moose" : "0", + "Text::CSV" : "0", + "Try::Tiny" : "0", + "strict" : "0", + "warnings" : "0" + } + }, + "test" : { + "recommends" : { + "CPAN::Meta" : "2.120900" + }, + "requires" : { + "Env::Path" : "0.18", + "ExtUtils::MakeMaker" : "0", + "File::Spec" : "0", + "Test::Exception" : "0", + "Test::Files" : "0", + "Test::More" : "0", + "Test::Most" : "0" + } + } + }, + "provides" : { + "Bio::Tradis" : { + "file" : "lib/Bio/Tradis.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::AddTagsToSeq" : { + "file" : "lib/Bio/Tradis/AddTagsToSeq.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Analysis::Exceptions" : { + "file" : "lib/Bio/Tradis/Analysis/Exceptions.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Analysis::InsertSite" : { + "file" : "lib/Bio/Tradis/Analysis/InsertSite.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CombinePlots" : { + "file" : "lib/Bio/Tradis/CombinePlots.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::AddTags" : { + "file" : "lib/Bio/Tradis/CommandLine/AddTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::CheckTags" : { + "file" : "lib/Bio/Tradis/CommandLine/CheckTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::FilterFastqTags" : { + "file" : "lib/Bio/Tradis/CommandLine/FilterFastqTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::PlotCombine" : { + "file" : "lib/Bio/Tradis/CommandLine/PlotCombine.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::PlotTradis" : { + "file" : "lib/Bio/Tradis/CommandLine/PlotTradis.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::RemoveFastqTags" : { + "file" : "lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::RunMapping" : { + "file" : "lib/Bio/Tradis/CommandLine/RunMapping.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::TradisAnalysis" : { + "file" : "lib/Bio/Tradis/CommandLine/TradisAnalysis.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::CommandLine::TradisBam" : { + "file" : "lib/Bio/Tradis/CommandLine/TradisBam.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::DetectTags" : { + "file" : "lib/Bio/Tradis/DetectTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Exception" : { + "file" : "lib/Bio/Tradis/Exception.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::FilterTags" : { + "file" : "lib/Bio/Tradis/FilterTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Map" : { + "file" : "lib/Bio/Tradis/Map.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Parser::Bam" : { + "file" : "lib/Bio/Tradis/Parser/Bam.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Parser::Cigar" : { + "file" : "lib/Bio/Tradis/Parser/Cigar.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Parser::Fastq" : { + "file" : "lib/Bio/Tradis/Parser/Fastq.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::RemoveTags" : { + "file" : "lib/Bio/Tradis/RemoveTags.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::RunTradis" : { + "file" : "lib/Bio/Tradis/RunTradis.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::Samtools" : { + "file" : "lib/Bio/Tradis/Samtools.pm", + "version" : "v1.4.5" + }, + "Bio::Tradis::TradisPlot" : { + "file" : "lib/Bio/Tradis/TradisPlot.pm", + "version" : "v1.4.5" + } + }, + "release_status" : "stable", + "resources" : { + "homepage" : "http://www.sanger.ac.uk/", + "repository" : { + "type" : "git", + "url" : "https://github.com/sanger-pathogens/Bio-Tradis.git", + "web" : "https://github.com/sanger-pathogens/Bio-Tradis" + } + }, + "version" : "1.4.5", + "x_Dist_Zilla" : { + "perl" : { + "version" : "5.030000" + }, + "plugins" : [ + { + "class" : "Dist::Zilla::Plugin::MetaResources", + "name" : "MetaResources", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::RequiresExternal", + "name" : "RequiresExternal", + "version" : "1.008" + }, + { + "class" : "Dist::Zilla::Plugin::Git::Check", + "config" : { + "Dist::Zilla::Plugin::Git::Check" : { + "untracked_files" : "die" + }, + "Dist::Zilla::Role::Git::DirtyFiles" : { + "allow_dirty" : [ + "Changes", + "dist.ini" + ], + "allow_dirty_match" : [], + "changelog" : "Changes" + }, + "Dist::Zilla::Role::Git::Repo" : { + "git_version" : "2.24.0", + "repo_root" : "." + } + }, + "name" : "@Git/Check", + "version" : "2.046" + }, + { + "class" : "Dist::Zilla::Plugin::Git::Commit", + "config" : { + "Dist::Zilla::Plugin::Git::Commit" : { + "add_files_in" : [], + "commit_msg" : "v%V%n%n%c" + }, + "Dist::Zilla::Role::Git::DirtyFiles" : { + "allow_dirty" : [ + "Changes", + "dist.ini" + ], + "allow_dirty_match" : [], + "changelog" : "Changes" + }, + "Dist::Zilla::Role::Git::Repo" : { + "git_version" : "2.24.0", + "repo_root" : "." + }, + "Dist::Zilla::Role::Git::StringFormatter" : { + "time_zone" : "local" + } + }, + "name" : "@Git/Commit", + "version" : "2.046" + }, + { + "class" : "Dist::Zilla::Plugin::Git::Tag", + "config" : { + "Dist::Zilla::Plugin::Git::Tag" : { + "branch" : null, + "changelog" : "Changes", + "signed" : 0, + "tag" : "v1.4.5", + "tag_format" : "v%V", + "tag_message" : "v%V" + }, + "Dist::Zilla::Role::Git::Repo" : { + "git_version" : "2.24.0", + "repo_root" : "." + }, + "Dist::Zilla::Role::Git::StringFormatter" : { + "time_zone" : "local" + } + }, + "name" : "@Git/Tag", + "version" : "2.046" + }, + { + "class" : "Dist::Zilla::Plugin::Git::Push", + "config" : { + "Dist::Zilla::Plugin::Git::Push" : { + "push_to" : [ + "origin" + ], + "remotes_must_exist" : 1 + }, + "Dist::Zilla::Role::Git::Repo" : { + "git_version" : "2.24.0", + "repo_root" : "." + } + }, + "name" : "@Git/Push", + "version" : "2.046" + }, + { + "class" : "Dist::Zilla::Plugin::GatherDir", + "config" : { + "Dist::Zilla::Plugin::GatherDir" : { + "exclude_filename" : [], + "exclude_match" : [], + "follow_symlinks" : 0, + "include_dotfiles" : 0, + "prefix" : "", + "prune_directory" : [], + "root" : "." + } + }, + "name" : "@Starter/GatherDir", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::MetaYAML", + "name" : "@Starter/MetaYAML", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::MetaJSON", + "name" : "@Starter/MetaJSON", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::License", + "name" : "@Starter/License", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::ReadmeAnyFromPod", + "config" : { + "Dist::Zilla::Role::FileWatcher" : { + "version" : "0.006" + } + }, + "name" : "@Starter/ReadmeAnyFromPod", + "version" : "0.163250" + }, + { + "class" : "Dist::Zilla::Plugin::PodSyntaxTests", + "name" : "@Starter/PodSyntaxTests", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::Test::ReportPrereqs", + "name" : "@Starter/Test::ReportPrereqs", + "version" : "0.027" + }, + { + "class" : "Dist::Zilla::Plugin::Test::Compile", + "config" : { + "Dist::Zilla::Plugin::Test::Compile" : { + "bail_out_on_fail" : 0, + "fail_on_warning" : "author", + "fake_home" : 0, + "filename" : "xt/author/00-compile.t", + "module_finder" : [ + ":InstallModules" + ], + "needs_display" : 0, + "phase" : "develop", + "script_finder" : [ + ":PerlExecFiles" + ], + "skips" : [], + "switch" : [] + } + }, + "name" : "@Starter/Test::Compile", + "version" : "2.058" + }, + { + "class" : "Dist::Zilla::Plugin::MakeMaker", + "config" : { + "Dist::Zilla::Role::TestRunner" : { + "default_jobs" : 1 + } + }, + "name" : "@Starter/MakeMaker", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::Manifest", + "name" : "@Starter/Manifest", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::PruneCruft", + "name" : "@Starter/PruneCruft", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::ManifestSkip", + "name" : "@Starter/ManifestSkip", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::RunExtraTests", + "config" : { + "Dist::Zilla::Role::TestRunner" : { + "default_jobs" : 1 + } + }, + "name" : "@Starter/RunExtraTests", + "version" : "0.029" + }, + { + "class" : "Dist::Zilla::Plugin::TestRelease", + "name" : "@Starter/TestRelease", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::ConfirmRelease", + "name" : "@Starter/ConfirmRelease", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::UploadToCPAN", + "name" : "@Starter/UploadToCPAN", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::MetaConfig", + "name" : "@Starter/MetaConfig", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::MetaNoIndex", + "name" : "@Starter/MetaNoIndex", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::MetaProvides::Package", + "config" : { + "Dist::Zilla::Plugin::MetaProvides::Package" : { + "finder_objects" : [ + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : "@Starter/MetaProvides::Package/AUTOVIV/:InstallModulesPM", + "version" : "6.012" + } + ], + "include_underscores" : 0 + }, + "Dist::Zilla::Role::MetaProvider::Provider" : { + "$Dist::Zilla::Role::MetaProvider::Provider::VERSION" : "2.002004", + "inherit_missing" : 1, + "inherit_version" : 1, + "meta_noindex" : 1 + }, + "Dist::Zilla::Role::ModuleMetadata" : { + "Module::Metadata" : "1.000036", + "version" : "0.006" + } + }, + "name" : "@Starter/MetaProvides::Package", + "version" : "2.004003" + }, + { + "class" : "Dist::Zilla::Plugin::ShareDir", + "name" : "@Starter/ShareDir", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::ExecDir", + "name" : "@Starter/ExecDir", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::RunExtraTests", + "config" : { + "Dist::Zilla::Role::TestRunner" : { + "default_jobs" : 1 + } + }, + "name" : "RunExtraTests", + "version" : "0.029" + }, + { + "class" : "Dist::Zilla::Plugin::AutoPrereqs", + "name" : "AutoPrereqs", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FileFinder::ByName", + "name" : "BinNotR", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::PodWeaver", + "config" : { + "Dist::Zilla::Plugin::PodWeaver" : { + "finder" : [ + ":InstallModules", + "BinNotR" + ], + "plugins" : [ + { + "class" : "Pod::Weaver::Plugin::EnsurePod5", + "name" : "@CorePrep/EnsurePod5", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Plugin::H1Nester", + "name" : "@CorePrep/H1Nester", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Plugin::SingleEncoding", + "name" : "@Default/SingleEncoding", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Name", + "name" : "@Default/Name", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Version", + "name" : "@Default/Version", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Region", + "name" : "@Default/prelude", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Generic", + "name" : "SYNOPSIS", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Generic", + "name" : "DESCRIPTION", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Generic", + "name" : "OVERVIEW", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Collect", + "name" : "ATTRIBUTES", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Collect", + "name" : "METHODS", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Collect", + "name" : "FUNCTIONS", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Leftovers", + "name" : "@Default/Leftovers", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Region", + "name" : "@Default/postlude", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Authors", + "name" : "@Default/Authors", + "version" : "4.015" + }, + { + "class" : "Pod::Weaver::Section::Legal", + "name" : "@Default/Legal", + "version" : "4.015" + } + ] + } + }, + "name" : "PodWeaver", + "version" : "4.008" + }, + { + "class" : "Dist::Zilla::Plugin::PkgVersion", + "name" : "PkgVersion", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::Encoding", + "name" : "Encoding", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":InstallModules", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":IncModules", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":TestFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":ExtraTestFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":ExecFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":PerlExecFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":ShareFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":MainModule", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":AllFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : ":NoFiles", + "version" : "6.012" + }, + { + "class" : "Dist::Zilla::Plugin::FinderCode", + "name" : "@Starter/MetaProvides::Package/AUTOVIV/:InstallModulesPM", + "version" : "6.012" + } + ], + "zilla" : { + "class" : "Dist::Zilla::Dist::Builder", + "config" : { + "is_trial" : 0 + }, + "version" : "6.012" + } + }, + "x_generated_by_perl" : "v5.30.0", + "x_serialization_backend" : "Cpanel::JSON::XS version 4.17" +} + diff -Nru bio-tradis-1.4.1+dfsg/META.yml bio-tradis-1.4.5+dfsg2/META.yml --- bio-tradis-1.4.1+dfsg/META.yml 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/META.yml 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,482 @@ +--- +abstract: 'Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308' +author: + - 'Carla Cummins ' +build_requires: + Env::Path: '0.18' + ExtUtils::MakeMaker: '0' + File::Spec: '0' + Test::Exception: '0' + Test::Files: '0' + Test::More: '0' + Test::Most: '0' +configure_requires: + ExtUtils::MakeMaker: '0' +dynamic_config: 0 +generated_by: 'Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010' +license: gpl +meta-spec: + url: http://module-build.sourceforge.net/META-spec-v1.4.html + version: '1.4' +name: Bio-Tradis +no_index: + directory: + - eg + - examples + - inc + - share + - t + - xt +provides: + Bio::Tradis: + file: lib/Bio/Tradis.pm + version: v1.4.5 + Bio::Tradis::AddTagsToSeq: + file: lib/Bio/Tradis/AddTagsToSeq.pm + version: v1.4.5 + Bio::Tradis::Analysis::Exceptions: + file: lib/Bio/Tradis/Analysis/Exceptions.pm + version: v1.4.5 + Bio::Tradis::Analysis::InsertSite: + file: lib/Bio/Tradis/Analysis/InsertSite.pm + version: v1.4.5 + Bio::Tradis::CombinePlots: + file: lib/Bio/Tradis/CombinePlots.pm + version: v1.4.5 + Bio::Tradis::CommandLine::AddTags: + file: lib/Bio/Tradis/CommandLine/AddTags.pm + version: v1.4.5 + Bio::Tradis::CommandLine::CheckTags: + file: lib/Bio/Tradis/CommandLine/CheckTags.pm + version: v1.4.5 + Bio::Tradis::CommandLine::FilterFastqTags: + file: lib/Bio/Tradis/CommandLine/FilterFastqTags.pm + version: v1.4.5 + Bio::Tradis::CommandLine::PlotCombine: + file: lib/Bio/Tradis/CommandLine/PlotCombine.pm + version: v1.4.5 + Bio::Tradis::CommandLine::PlotTradis: + file: lib/Bio/Tradis/CommandLine/PlotTradis.pm + version: v1.4.5 + Bio::Tradis::CommandLine::RemoveFastqTags: + file: lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm + version: v1.4.5 + Bio::Tradis::CommandLine::RunMapping: + file: lib/Bio/Tradis/CommandLine/RunMapping.pm + version: v1.4.5 + Bio::Tradis::CommandLine::TradisAnalysis: + file: lib/Bio/Tradis/CommandLine/TradisAnalysis.pm + version: v1.4.5 + Bio::Tradis::CommandLine::TradisBam: + file: lib/Bio/Tradis/CommandLine/TradisBam.pm + version: v1.4.5 + Bio::Tradis::DetectTags: + file: lib/Bio/Tradis/DetectTags.pm + version: v1.4.5 + Bio::Tradis::Exception: + file: lib/Bio/Tradis/Exception.pm + version: v1.4.5 + Bio::Tradis::FilterTags: + file: lib/Bio/Tradis/FilterTags.pm + version: v1.4.5 + Bio::Tradis::Map: + file: lib/Bio/Tradis/Map.pm + version: v1.4.5 + Bio::Tradis::Parser::Bam: + file: lib/Bio/Tradis/Parser/Bam.pm + version: v1.4.5 + Bio::Tradis::Parser::Cigar: + file: lib/Bio/Tradis/Parser/Cigar.pm + version: v1.4.5 + Bio::Tradis::Parser::Fastq: + file: lib/Bio/Tradis/Parser/Fastq.pm + version: v1.4.5 + Bio::Tradis::RemoveTags: + file: lib/Bio/Tradis/RemoveTags.pm + version: v1.4.5 + Bio::Tradis::RunTradis: + file: lib/Bio/Tradis/RunTradis.pm + version: v1.4.5 + Bio::Tradis::Samtools: + file: lib/Bio/Tradis/Samtools.pm + version: v1.4.5 + Bio::Tradis::TradisPlot: + file: lib/Bio/Tradis/TradisPlot.pm + version: v1.4.5 +requires: + Bio::Seq: '0' + Bio::SeqIO: '0' + Cwd: '0' + Data::Dumper: '0' + Exception::Class: '0' + File::Basename: '0' + File::Path: '0' + File::Spec: '0' + File::Temp: '0' + FindBin: '0' + Getopt::Long: '0' + Moose: '0' + Text::CSV: '0' + Try::Tiny: '0' + strict: '0' + warnings: '0' +resources: + homepage: http://www.sanger.ac.uk/ + repository: https://github.com/sanger-pathogens/Bio-Tradis.git +version: 1.4.5 +x_Dist_Zilla: + perl: + version: '5.030000' + plugins: + - + class: Dist::Zilla::Plugin::MetaResources + name: MetaResources + version: '6.012' + - + class: Dist::Zilla::Plugin::RequiresExternal + name: RequiresExternal + version: '1.008' + - + class: Dist::Zilla::Plugin::Git::Check + config: + Dist::Zilla::Plugin::Git::Check: + untracked_files: die + Dist::Zilla::Role::Git::DirtyFiles: + allow_dirty: + - Changes + - dist.ini + allow_dirty_match: [] + changelog: Changes + Dist::Zilla::Role::Git::Repo: + git_version: 2.24.0 + repo_root: . + name: '@Git/Check' + version: '2.046' + - + class: Dist::Zilla::Plugin::Git::Commit + config: + Dist::Zilla::Plugin::Git::Commit: + add_files_in: [] + commit_msg: v%V%n%n%c + Dist::Zilla::Role::Git::DirtyFiles: + allow_dirty: + - Changes + - dist.ini + allow_dirty_match: [] + changelog: Changes + Dist::Zilla::Role::Git::Repo: + git_version: 2.24.0 + repo_root: . + Dist::Zilla::Role::Git::StringFormatter: + time_zone: local + name: '@Git/Commit' + version: '2.046' + - + class: Dist::Zilla::Plugin::Git::Tag + config: + Dist::Zilla::Plugin::Git::Tag: + branch: ~ + changelog: Changes + signed: 0 + tag: v1.4.5 + tag_format: v%V + tag_message: v%V + Dist::Zilla::Role::Git::Repo: + git_version: 2.24.0 + repo_root: . + Dist::Zilla::Role::Git::StringFormatter: + time_zone: local + name: '@Git/Tag' + version: '2.046' + - + class: Dist::Zilla::Plugin::Git::Push + config: + Dist::Zilla::Plugin::Git::Push: + push_to: + - origin + remotes_must_exist: 1 + Dist::Zilla::Role::Git::Repo: + git_version: 2.24.0 + repo_root: . + name: '@Git/Push' + version: '2.046' + - + class: Dist::Zilla::Plugin::GatherDir + config: + Dist::Zilla::Plugin::GatherDir: + exclude_filename: [] + exclude_match: [] + follow_symlinks: 0 + include_dotfiles: 0 + prefix: '' + prune_directory: [] + root: . + name: '@Starter/GatherDir' + version: '6.012' + - + class: Dist::Zilla::Plugin::MetaYAML + name: '@Starter/MetaYAML' + version: '6.012' + - + class: Dist::Zilla::Plugin::MetaJSON + name: '@Starter/MetaJSON' + version: '6.012' + - + class: Dist::Zilla::Plugin::License + name: '@Starter/License' + version: '6.012' + - + class: Dist::Zilla::Plugin::ReadmeAnyFromPod + config: + Dist::Zilla::Role::FileWatcher: + version: '0.006' + name: '@Starter/ReadmeAnyFromPod' + version: '0.163250' + - + class: Dist::Zilla::Plugin::PodSyntaxTests + name: '@Starter/PodSyntaxTests' + version: '6.012' + - + class: Dist::Zilla::Plugin::Test::ReportPrereqs + name: '@Starter/Test::ReportPrereqs' + version: '0.027' + - + class: Dist::Zilla::Plugin::Test::Compile + config: + Dist::Zilla::Plugin::Test::Compile: + bail_out_on_fail: '0' + fail_on_warning: author + fake_home: 0 + filename: xt/author/00-compile.t + module_finder: + - ':InstallModules' + needs_display: 0 + phase: develop + script_finder: + - ':PerlExecFiles' + skips: [] + switch: [] + name: '@Starter/Test::Compile' + version: '2.058' + - + class: Dist::Zilla::Plugin::MakeMaker + config: + Dist::Zilla::Role::TestRunner: + default_jobs: 1 + name: '@Starter/MakeMaker' + version: '6.012' + - + class: Dist::Zilla::Plugin::Manifest + name: '@Starter/Manifest' + version: '6.012' + - + class: Dist::Zilla::Plugin::PruneCruft + name: '@Starter/PruneCruft' + version: '6.012' + - + class: Dist::Zilla::Plugin::ManifestSkip + name: '@Starter/ManifestSkip' + version: '6.012' + - + class: Dist::Zilla::Plugin::RunExtraTests + config: + Dist::Zilla::Role::TestRunner: + default_jobs: 1 + name: '@Starter/RunExtraTests' + version: '0.029' + - + class: Dist::Zilla::Plugin::TestRelease + name: '@Starter/TestRelease' + version: '6.012' + - + class: Dist::Zilla::Plugin::ConfirmRelease + name: '@Starter/ConfirmRelease' + version: '6.012' + - + class: Dist::Zilla::Plugin::UploadToCPAN + name: '@Starter/UploadToCPAN' + version: '6.012' + - + class: Dist::Zilla::Plugin::MetaConfig + name: '@Starter/MetaConfig' + version: '6.012' + - + class: Dist::Zilla::Plugin::MetaNoIndex + name: '@Starter/MetaNoIndex' + version: '6.012' + - + class: Dist::Zilla::Plugin::MetaProvides::Package + config: + Dist::Zilla::Plugin::MetaProvides::Package: + finder_objects: + - + class: Dist::Zilla::Plugin::FinderCode + name: '@Starter/MetaProvides::Package/AUTOVIV/:InstallModulesPM' + version: '6.012' + include_underscores: 0 + Dist::Zilla::Role::MetaProvider::Provider: + $Dist::Zilla::Role::MetaProvider::Provider::VERSION: '2.002004' + inherit_missing: '1' + inherit_version: '1' + meta_noindex: '1' + Dist::Zilla::Role::ModuleMetadata: + Module::Metadata: '1.000036' + version: '0.006' + name: '@Starter/MetaProvides::Package' + version: '2.004003' + - + class: Dist::Zilla::Plugin::ShareDir + name: '@Starter/ShareDir' + version: '6.012' + - + class: Dist::Zilla::Plugin::ExecDir + name: '@Starter/ExecDir' + version: '6.012' + - + class: Dist::Zilla::Plugin::RunExtraTests + config: + Dist::Zilla::Role::TestRunner: + default_jobs: 1 + name: RunExtraTests + version: '0.029' + - + class: Dist::Zilla::Plugin::AutoPrereqs + name: AutoPrereqs + version: '6.012' + - + class: Dist::Zilla::Plugin::FileFinder::ByName + name: BinNotR + version: '6.012' + - + class: Dist::Zilla::Plugin::PodWeaver + config: + Dist::Zilla::Plugin::PodWeaver: + finder: + - ':InstallModules' + - BinNotR + plugins: + - + class: Pod::Weaver::Plugin::EnsurePod5 + name: '@CorePrep/EnsurePod5' + version: '4.015' + - + class: Pod::Weaver::Plugin::H1Nester + name: '@CorePrep/H1Nester' + version: '4.015' + - + class: Pod::Weaver::Plugin::SingleEncoding + name: '@Default/SingleEncoding' + version: '4.015' + - + class: Pod::Weaver::Section::Name + name: '@Default/Name' + version: '4.015' + - + class: Pod::Weaver::Section::Version + name: '@Default/Version' + version: '4.015' + - + class: Pod::Weaver::Section::Region + name: '@Default/prelude' + version: '4.015' + - + class: Pod::Weaver::Section::Generic + name: SYNOPSIS + version: '4.015' + - + class: Pod::Weaver::Section::Generic + name: DESCRIPTION + version: '4.015' + - + class: Pod::Weaver::Section::Generic + name: OVERVIEW + version: '4.015' + - + class: Pod::Weaver::Section::Collect + name: ATTRIBUTES + version: '4.015' + - + class: Pod::Weaver::Section::Collect + name: METHODS + version: '4.015' + - + class: Pod::Weaver::Section::Collect + name: FUNCTIONS + version: '4.015' + - + class: Pod::Weaver::Section::Leftovers + name: '@Default/Leftovers' + version: '4.015' + - + class: Pod::Weaver::Section::Region + name: '@Default/postlude' + version: '4.015' + - + class: Pod::Weaver::Section::Authors + name: '@Default/Authors' + version: '4.015' + - + class: Pod::Weaver::Section::Legal + name: '@Default/Legal' + version: '4.015' + name: PodWeaver + version: '4.008' + - + class: Dist::Zilla::Plugin::PkgVersion + name: PkgVersion + version: '6.012' + - + class: Dist::Zilla::Plugin::Encoding + name: Encoding + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':InstallModules' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':IncModules' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':TestFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':ExtraTestFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':ExecFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':PerlExecFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':ShareFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':MainModule' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':AllFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: ':NoFiles' + version: '6.012' + - + class: Dist::Zilla::Plugin::FinderCode + name: '@Starter/MetaProvides::Package/AUTOVIV/:InstallModulesPM' + version: '6.012' + zilla: + class: Dist::Zilla::Dist::Builder + config: + is_trial: '0' + version: '6.012' +x_generated_by_perl: v5.30.0 +x_serialization_backend: 'YAML::Tiny version 1.73' diff -Nru bio-tradis-1.4.1+dfsg/README bio-tradis-1.4.5+dfsg2/README --- bio-tradis-1.4.1+dfsg/README 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/README 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,42 @@ +NAME + + Bio::Tradis - Bio-Tradis contains a set of tools to analyse the output + from TraDIS analyses. For more information on the TraDIS method, see + http://genome.cshlp.org/content/19/12/2308 + +VERSION + + version 1.4.5 + +SYNOPSIS + + Bio-Tradis provides functionality to: + + * detect TraDIS tags in a BAM file - Bio::Tradis::DetectTags + + * add the tags to the reads - Bio::Tradis::AddTagsToSeq + + * filter reads in a FastQ file containing a user defined tag - + Bio::Tradis::FilterTags + + * remove tags - Bio::Tradis::RemoveTags + + * map to a reference genome - Bio::Tradis::Map + + * create an insertion site plot file - Bio::Tradis::TradisPlot + + Most of these functions are available as standalone scripts or as perl + modules. + +AUTHOR + + Carla Cummins + +COPYRIGHT AND LICENSE + + This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. + + This is free software, licensed under: + + The GNU General Public License, Version 3, June 2007 + diff -Nru bio-tradis-1.4.1+dfsg/README.md bio-tradis-1.4.5+dfsg2/README.md --- bio-tradis-1.4.1+dfsg/README.md 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/README.md 2019-12-04 14:40:22.000000000 +0000 @@ -4,6 +4,8 @@ [![Build Status](https://travis-ci.org/sanger-pathogens/Bio-Tradis.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Bio-Tradis) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/Bio-Tradis/blob/master/software_license) [![status](https://img.shields.io/badge/Bioinformatics-10.1093-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btw022) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biotradis/README.html) +[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/biotradis) [![Docker Build Status](https://img.shields.io/docker/build/sangerpathogens/bio-tradis.svg)](https://hub.docker.com/r/sangerpathogens/bio-tradis) [![Docker Pulls](https://img.shields.io/docker/pulls/sangerpathogens/bio-tradis.svg)](https://hub.docker.com/r/sangerpathogens/bio-tradis) [![codecov](https://codecov.io/gh/sanger-pathogens/bio-tradis/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/bio-tradis) @@ -14,6 +16,7 @@ * [Required dependencies](#required-dependencies) * [Bioconda](#bioconda) * [Docker](#docker) + * [Running the tests](#running-the-tests) * [Usage](#usage) * [Scripts](#scripts) * [Analysis Scripts](#analysis-scripts) @@ -32,6 +35,7 @@ Bio-Tradis has the following dependencies: ### Required dependencies +* bwa * smalt * samtools * tabix @@ -44,17 +48,8 @@ Install conda and enable the bioconda channel. ``` -conda config --add channels r -conda config --add channels defaults -conda config --add channels conda-forge -conda config --add channels bioconda -conda install r smalt samtools perl-app-cpanminus - -sudo cpanm -f Bio::Tradis -R -source("http://bioconductor.org/biocLite.R") -biocLite() -biocLite(c("edgeR","getopt", "MASS")) +conda install-c bioconda biotradis=1.4.1.dev + ``` ### Docker @@ -66,6 +61,11 @@ docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/bio-tradis bacteria_tradis -h +### Running the tests +The test can be run with dzil from the top level directory: + +`dzil test` + ## Usage For command-line usage instructions, please see the tutorial in the file "BioTraDISTutorial.pdf". Note that default parameters are for comparative experiments, and will need to be modified for gene essentiality studies. @@ -88,7 +88,7 @@ * `filter_tradis_tags` - Create a fastq file containing reads that match the supplied tag * `remove_tradis_tags` - Creates a fastq file containing reads with the supplied tag removed from the sequences * `tradis_plot` - Creates an gzipped insertion site plot -* `bacteria_tradis` - Runs complete analysis, starting with a fastq file and produces mapped BAM files and plot files for each file in the given file list and a statistical summary of all files. Note that the -f option expects a text file containing a list of fastq files, one per line. +* `bacteria_tradis` - Runs complete analysis, starting with a fastq file and produces mapped BAM files and plot files for each file in the given file list and a statistical summary of all files. Note that the -f option expects a text file containing a list of fastq files, one per line. This script can be run with or without supplying tags. A help menu for each script can be accessed by running the script with no parameters. @@ -155,15 +155,16 @@ * Methods: * `index_ref` - create index files of the reference genome. These are required for the mapping step. Only skip this step if index files already - exist. -k and -s options for referencing are calculated based + exist. If SMALT is used as the aligner -sk and -ss options for referencing are calculated based on the length of the reads being mapped: - * <70 : `-k 13 -s 4` - * >70 & <100 : `-k 13 -s 6` - * >100 : `-k 20 -s 13` + * <70 : `-sk 13 -ss 4` + * >70 & <100 : `-sk 13 -ss 6` + * >100 : `-sk 20 -ss 13` * `do_mapping` - map `fastqfile` to `reference`. Options used for mapping are: - `-r -1, -x and -y 0.96` + `-k the min seed length for BWA` + `-s (for using SMALT as alternative aligner) -r -1, -x and -y 0.96 for SMALT (see SMALT manual)` - For more information on the mapping and indexing options discussed here, see the SMALT manual (ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf) + For more information on the mapping and indexing options discussed here, see the BWA manual (http://rothlab.ucdavis.edu/howto/attachments/bwa_manpage.pdf) and/or SMALT manual (ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-manual-0.7.4.pdf) __Bio::Tradis::TradisPlot__ * Required parameters: @@ -253,4 +254,4 @@ If you use this software please cite: -"The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries", Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge G, Quail MA, Keane JA, Parkhill J. Bioinformatics. 2016 Apr 1;32(7):1109-11. doi: [10.1093/bioinformatics/btw022](https://doi.org/10.1093/bioinformatics/btw022). Epub 2016 Jan 21. \ No newline at end of file +"The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries", Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge G, Quail MA, Keane JA, Parkhill J. Bioinformatics. 2016 Apr 1;32(7):1109-11. doi: [10.1093/bioinformatics/btw022](https://doi.org/10.1093/bioinformatics/btw022). Epub 2016 Jan 21. diff -Nru bio-tradis-1.4.1+dfsg/source_path bio-tradis-1.4.5+dfsg2/source_path --- bio-tradis-1.4.1+dfsg/source_path 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/source_path 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,22 @@ +SMALT_VERSION="0.7.6" +BWA_VERSION="0.7.17" +TABIX_VERSION="master" +SAMTOOLS_VERSION="1.3" + +smalt_dir=$(pwd)/"smalt-${SMALT_VERSION}-bin" +bwa_dir=$(pwd)/"bwa-${BWA_VERSION}" +tabix_dir=$(pwd)/"tabix-$TABIX_VERSION" +samtools_dir=$(pwd)/"samtools-$SAMTOOLS_VERSION" + +update_path () { + new_dir=$1 + if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then + export PATH=${new_dir}:${PATH} + fi +} + +update_path ${smalt_dir} +update_path ${bwa_dir} +update_path "${tabix_dir}" +update_path "${samtools_dir}" + diff -Nru bio-tradis-1.4.1+dfsg/t/00-report-prereqs.dd bio-tradis-1.4.5+dfsg2/t/00-report-prereqs.dd --- bio-tradis-1.4.1+dfsg/t/00-report-prereqs.dd 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/00-report-prereqs.dd 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,53 @@ +do { my $x = { + 'configure' => { + 'requires' => { + 'ExtUtils::MakeMaker' => '0' + } + }, + 'develop' => { + 'requires' => { + 'File::Spec' => '0', + 'IO::Handle' => '0', + 'IPC::Open3' => '0', + 'Test::More' => '0', + 'Test::Pod' => '1.41', + 'perl' => '5.006' + } + }, + 'runtime' => { + 'requires' => { + 'Bio::Seq' => '0', + 'Bio::SeqIO' => '0', + 'Cwd' => '0', + 'Data::Dumper' => '0', + 'Exception::Class' => '0', + 'File::Basename' => '0', + 'File::Path' => '0', + 'File::Spec' => '0', + 'File::Temp' => '0', + 'FindBin' => '0', + 'Getopt::Long' => '0', + 'Moose' => '0', + 'Text::CSV' => '0', + 'Try::Tiny' => '0', + 'strict' => '0', + 'warnings' => '0' + } + }, + 'test' => { + 'recommends' => { + 'CPAN::Meta' => '2.120900' + }, + 'requires' => { + 'Env::Path' => '0.18', + 'ExtUtils::MakeMaker' => '0', + 'File::Spec' => '0', + 'Test::Exception' => '0', + 'Test::Files' => '0', + 'Test::More' => '0', + 'Test::Most' => '0' + } + } + }; + $x; + } \ No newline at end of file diff -Nru bio-tradis-1.4.1+dfsg/t/00-report-prereqs.t bio-tradis-1.4.5+dfsg2/t/00-report-prereqs.t --- bio-tradis-1.4.1+dfsg/t/00-report-prereqs.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/00-report-prereqs.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,193 @@ +#!perl + +use strict; +use warnings; + +# This test was generated by Dist::Zilla::Plugin::Test::ReportPrereqs 0.027 + +use Test::More tests => 1; + +use ExtUtils::MakeMaker; +use File::Spec; + +# from $version::LAX +my $lax_version_re = + qr/(?: undef | (?: (?:[0-9]+) (?: \. | (?:\.[0-9]+) (?:_[0-9]+)? )? + | + (?:\.[0-9]+) (?:_[0-9]+)? + ) | (?: + v (?:[0-9]+) (?: (?:\.[0-9]+)+ (?:_[0-9]+)? )? + | + (?:[0-9]+)? (?:\.[0-9]+){2,} (?:_[0-9]+)? + ) + )/x; + +# hide optional CPAN::Meta modules from prereq scanner +# and check if they are available +my $cpan_meta = "CPAN::Meta"; +my $cpan_meta_pre = "CPAN::Meta::Prereqs"; +my $HAS_CPAN_META = eval "require $cpan_meta; $cpan_meta->VERSION('2.120900')" && eval "require $cpan_meta_pre"; ## no critic + +# Verify requirements? +my $DO_VERIFY_PREREQS = 1; + +sub _max { + my $max = shift; + $max = ( $_ > $max ) ? $_ : $max for @_; + return $max; +} + +sub _merge_prereqs { + my ($collector, $prereqs) = @_; + + # CPAN::Meta::Prereqs object + if (ref $collector eq $cpan_meta_pre) { + return $collector->with_merged_prereqs( + CPAN::Meta::Prereqs->new( $prereqs ) + ); + } + + # Raw hashrefs + for my $phase ( keys %$prereqs ) { + for my $type ( keys %{ $prereqs->{$phase} } ) { + for my $module ( keys %{ $prereqs->{$phase}{$type} } ) { + $collector->{$phase}{$type}{$module} = $prereqs->{$phase}{$type}{$module}; + } + } + } + + return $collector; +} + +my @include = qw( + +); + +my @exclude = qw( + +); + +# Add static prereqs to the included modules list +my $static_prereqs = do './t/00-report-prereqs.dd'; + +# Merge all prereqs (either with ::Prereqs or a hashref) +my $full_prereqs = _merge_prereqs( + ( $HAS_CPAN_META ? $cpan_meta_pre->new : {} ), + $static_prereqs +); + +# Add dynamic prereqs to the included modules list (if we can) +my ($source) = grep { -f } 'MYMETA.json', 'MYMETA.yml'; +my $cpan_meta_error; +if ( $source && $HAS_CPAN_META + && (my $meta = eval { CPAN::Meta->load_file($source) } ) +) { + $full_prereqs = _merge_prereqs($full_prereqs, $meta->prereqs); +} +else { + $cpan_meta_error = $@; # capture error from CPAN::Meta->load_file($source) + $source = 'static metadata'; +} + +my @full_reports; +my @dep_errors; +my $req_hash = $HAS_CPAN_META ? $full_prereqs->as_string_hash : $full_prereqs; + +# Add static includes into a fake section +for my $mod (@include) { + $req_hash->{other}{modules}{$mod} = 0; +} + +for my $phase ( qw(configure build test runtime develop other) ) { + next unless $req_hash->{$phase}; + next if ($phase eq 'develop' and not $ENV{AUTHOR_TESTING}); + + for my $type ( qw(requires recommends suggests conflicts modules) ) { + next unless $req_hash->{$phase}{$type}; + + my $title = ucfirst($phase).' '.ucfirst($type); + my @reports = [qw/Module Want Have/]; + + for my $mod ( sort keys %{ $req_hash->{$phase}{$type} } ) { + next if $mod eq 'perl'; + next if grep { $_ eq $mod } @exclude; + + my $file = $mod; + $file =~ s{::}{/}g; + $file .= ".pm"; + my ($prefix) = grep { -e File::Spec->catfile($_, $file) } @INC; + + my $want = $req_hash->{$phase}{$type}{$mod}; + $want = "undef" unless defined $want; + $want = "any" if !$want && $want == 0; + + my $req_string = $want eq 'any' ? 'any version required' : "version '$want' required"; + + if ($prefix) { + my $have = MM->parse_version( File::Spec->catfile($prefix, $file) ); + $have = "undef" unless defined $have; + push @reports, [$mod, $want, $have]; + + if ( $DO_VERIFY_PREREQS && $HAS_CPAN_META && $type eq 'requires' ) { + if ( $have !~ /\A$lax_version_re\z/ ) { + push @dep_errors, "$mod version '$have' cannot be parsed ($req_string)"; + } + elsif ( ! $full_prereqs->requirements_for( $phase, $type )->accepts_module( $mod => $have ) ) { + push @dep_errors, "$mod version '$have' is not in required range '$want'"; + } + } + } + else { + push @reports, [$mod, $want, "missing"]; + + if ( $DO_VERIFY_PREREQS && $type eq 'requires' ) { + push @dep_errors, "$mod is not installed ($req_string)"; + } + } + } + + if ( @reports ) { + push @full_reports, "=== $title ===\n\n"; + + my $ml = _max( map { length $_->[0] } @reports ); + my $wl = _max( map { length $_->[1] } @reports ); + my $hl = _max( map { length $_->[2] } @reports ); + + if ($type eq 'modules') { + splice @reports, 1, 0, ["-" x $ml, "", "-" x $hl]; + push @full_reports, map { sprintf(" %*s %*s\n", -$ml, $_->[0], $hl, $_->[2]) } @reports; + } + else { + splice @reports, 1, 0, ["-" x $ml, "-" x $wl, "-" x $hl]; + push @full_reports, map { sprintf(" %*s %*s %*s\n", -$ml, $_->[0], $wl, $_->[1], $hl, $_->[2]) } @reports; + } + + push @full_reports, "\n"; + } + } +} + +if ( @full_reports ) { + diag "\nVersions for all modules listed in $source (including optional ones):\n\n", @full_reports; +} + +if ( $cpan_meta_error || @dep_errors ) { + diag "\n*** WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING ***\n"; +} + +if ( $cpan_meta_error ) { + my ($orig_source) = grep { -f } 'MYMETA.json', 'MYMETA.yml'; + diag "\nCPAN::Meta->load_file('$orig_source') failed with: $cpan_meta_error\n"; +} + +if ( @dep_errors ) { + diag join("\n", + "\nThe following REQUIRED prerequisites were not satisfied:\n", + @dep_errors, + "\n" + ); +} + +pass; + +# vim: ts=4 sts=4 sw=4 et: diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/CommandLine/TradisAnalysis.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/CommandLine/TradisAnalysis.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/CommandLine/TradisAnalysis.t 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/CommandLine/TradisAnalysis.t 2019-12-04 14:40:22.000000000 +0000 @@ -23,7 +23,7 @@ ok( my $obj = Bio::Tradis::CommandLine::TradisAnalysis->new( args => ['-f', 't/data/CommandLine/fastq.list', '-t', - "TAAGAGTCAG", '-r', "t/data/RunTradis/smallref.fa"], + "TAAGAGTCAG", '-r', "t/data/RunTradisSmalt/smallref.fa"], script_name => 'bacteria_tradis_test', _output_directory => $output_directory ), @@ -46,7 +46,7 @@ $obj = Bio::Tradis::CommandLine::TradisAnalysis->new( args => ['-f', 't/data/CommandLine/fastq.list', '-t', - "CGCACAGCCG", '-r', "t/data/RunTradis/smallref.fa"], + "CGCACAGCCG", '-r', "t/data/RunTradisSmalt/smallref.fa"], script_name => 'bacteria_tradis_test', _output_directory => $output_directory ); @@ -71,7 +71,7 @@ $obj = Bio::Tradis::CommandLine::TradisAnalysis->new( args => ['-f', 't/data/CommandLine/fastq.list', '-t', - "AAAAAAAAAA", '-r', "t/data/RunTradis/smallref.fa"], + "AAAAAAAAAA", '-r', "t/data/RunTradisSmalt/smallref.fa"], script_name => 'bacteria_tradis_test', _output_directory => $output_directory ); @@ -88,4 +88,4 @@ is( $line_count, 0, "neither input fastq has reads with tag"); rmtree($output_directory); -done_testing(); +done_testing(); \ No newline at end of file diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/Map.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/Map.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/Map.t 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/Map.t 2019-12-04 14:40:22.000000000 +0000 @@ -29,7 +29,8 @@ fastqfile => $fastqfile, reference => $ref, refname => $refname, - outfile => $outfile + outfile => $outfile, + smalt => 1 ), 'creating object' ); @@ -37,13 +38,41 @@ ok( -e 't/data/Map/test.ref.sma', 'checking index file existence' ); ok( -e 't/data/Map/test.ref.smi', 'checking index file existence' ); -ok( $obj->do_mapping, 'testing reference indexing' ); +ok( $obj->do_mapping, 'testing smalt mapping' ); ok( -e 't/data/Map/mapped.out', 'checking index file existence' ); system("grep -v ^\@ t/data/Map/mapped.out > mapped.nohead.out"); -system("grep -v ^\@ t/data/Map/expected.mapped > expected.nohead.mapped"); +system("grep -v ^\@ t/data/Map/expected.smalt.mapped > expected.smalt.nohead.mapped"); compare_ok( 'mapped.nohead.out', - 'expected.nohead.mapped', + 'expected.smalt.nohead.mapped', + 'checking file contents' +); + +ok( + $obj = Bio::Tradis::Map->new( + fastqfile => $fastqfile, + reference => $ref, + refname => $refname, + outfile => $outfile, + smalt => 0 + ), + 'creating object' +); +ok( $obj->index_ref, 'testing reference indexing' ); +ok( -e 't/data/Map/smallref.fa.amb', 'checking index file existence' ); +ok( -e 't/data/Map/smallref.fa.ann', 'checking index file existence' ); +ok( -e 't/data/Map/smallref.fa.bwt', 'checking index file existence' ); +ok( -e 't/data/Map/smallref.fa.pac', 'checking index file existence' ); +ok( -e 't/data/Map/smallref.fa.sa', 'checking index file existence' ); + + +ok( $obj->do_mapping, 'testing bwa mapping' ); +ok( -e 't/data/Map/mapped.out', 'checking index file existence' ); +system("grep -v ^\@ t/data/Map/mapped.out > mapped.nohead.out"); +system("grep -v ^\@ t/data/Map/expected.bwa.mapped > expected.bwa.nohead.mapped"); +compare_ok( + 'mapped.nohead.out', + 'expected.bwa.nohead.mapped', 'checking file contents' ); @@ -54,6 +83,7 @@ reference => $ref, refname => $refname, outfile => $outfile, + smalt => 1, smalt_k => 10, smalt_s => 10, smalt_y => 0.9 @@ -61,17 +91,21 @@ 'creating object' ); -my $index_cmd = $obj->index_ref; -my $index_exp = "smalt index -k 10 -s 10 $refname $ref > /dev/null 2>&1"; -is( $index_cmd, $index_exp, "indexing args correct" ); - -my $map_cmd = $obj->do_mapping; -my $map_exp = "smalt map -n 1 -x -r -1 -y 0.9 $refname $fastqfile 1> $outfile 2> smalt.stderr"; -is( $map_cmd, $map_exp, "mapping args correct" ); - +my $index_smalt_cmd = $obj->index_ref; +my $index_smalt_exp = "smalt index -k 10 -s 10 $refname $ref > /dev/null 2>&1"; +is( $index_smalt_cmd, $index_smalt_exp, "indexing args correct" ); + +my $map_smalt_cmd = $obj->do_mapping; +my $map_smalt_exp = "smalt map -n 1 -x -r -1 -y 0.9 $refname $fastqfile 1> $outfile 2> align.stderr"; +is( $map_smalt_cmd, $map_smalt_exp, "mapping args correct" ); unlink('t/data/Map/test.ref.sma'); unlink('t/data/Map/test.ref.smi'); unlink('t/data/Map/mapped.out'); +unlink('t/data/Map/smallref.fa.amb'); +unlink('t/data/Map/smallref.fa.ann'); +unlink('t/data/Map/smallref.fa.bwt'); +unlink('t/data/Map/smallref.fa.pac'); +unlink('t/data/Map/smallref.fa.sa'); done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisBWA.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisBWA.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisBWA.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,275 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use Cwd; +use File::Path 'rmtree'; +use File::Temp; +use Test::Files qw(compare_ok); + +BEGIN { unshift( @INC, './lib' ) } +BEGIN { unshift( @INC, '../lib' ) } + +BEGIN { + use Test::Most; + use Test::Exception; + use_ok('Bio::Tradis::RunTradis'); +} + +my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_tests_XXXXX', + CLEANUP => 0, + DIR => cwd() ); +my $output_directory = $output_directory_obj->dirname; +my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +my $temp_directory = $temp_directory_obj->dirname(); + +my ( $obj, $fastqfile, $stats_handle, $ref, $tag, $outfile, $aligner); + +# First, test all parts and complete pipeline without mismatch + +$fastqfile = "t/data/RunTradisBWA/test.tagged.fastq"; +$ref = "t/data/RunTradisBWA/smallref.fa"; +$tag = "TAAGAGTCAG"; +$outfile = "test.plot"; +$aligner = 0; +open( $stats_handle, '>', "$output_directory/test.stats" ); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files, no mismatch' +); + +# Filtering step +ok( $obj->_filter, 'testing filtering step' ); +ok( + -e "$temp_directory/filter.fastq", + 'checking filtered file existence - Normal files, no mismatch' +); +compare_ok( + "$temp_directory/filter.fastq", + 't/data/RunTradisBWA/filtered.fastq', + 'checking filtered file contents - Normal files, no mismatch' +); + +# Check filtering step +ok( $obj->_check_filter, 'testing check filtering step' ); +system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads'; +system("touch $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty'; +system("echo foo > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines'; +system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq'; +system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short'; +system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq"); +ok( $obj->_check_filter, 'check very basic filtered reads validation'); +system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq"); + +# Tag removal +ok( $obj->_remove, 'testing tag removal' ); +ok( -e "$temp_directory/tags_removed.fastq", + 'checking de-tagged file existence - Normal files, no mismatch' ); +compare_ok( + "$temp_directory/tags_removed.fastq", + 't/data/RunTradisBWA/notags.fastq', + 'checking de-tagged file contents - Normal files, no mismatch' +); + +# Mapping +ok( $obj->_map, 'testing mapping' ); +ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' ); +`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`; +`grep -v "\@PG" t/data/RunTradisBWA/mapped.sam > $output_directory/tmp2.sam`; +compare_ok( + "$output_directory/tmp1.sam", + "$output_directory/tmp2.sam", + 'checking mapped file contents' +); + +# Conversion +ok( $obj->_sam2bam, 'testing SAM/BAM conversion' ); +ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' ); + +# Sorting +ok( $obj->_sort_bam, 'testing BAM sorting' ); +ok( -e "$temp_directory/mapped.sort.bam", + 'checking sorted BAM existence - Normal files, no mismatch' ); +ok( -e "$temp_directory/mapped.sort.bam.bai", + 'checking indexed BAM existence - Normal files, no mismatch' ); + +#Bamcheck +ok( $obj->_bamcheck, 'testing bamcheck' ); +ok( -e "$temp_directory/mapped.bamcheck", + 'checking bamcheck file existence - Normal files, no mismatch' ); + +# Plot +ok( $obj->_make_plot, 'testing plotting' ); +ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system( +"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped" +); +system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking plot file contents - Normal files, no mismatch' +); + + +# Complete pipeline +ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline file contents - Normal files, no mismatch' +); + +unlink("$temp_directory/filter.fastq"); +unlink("$temp_directory/tags_removed.fastq"); + +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + +# Test complete pipeline with 1 mismatch allowed + +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + mismatch => 1, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files one mismatch' +); + +ok( $obj->run_tradis, 'testing complete analysis with mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files one mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); + + +system("gunzip -c t/data/RunTradisBWA/expected.1mm.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline with mismatch file contents - Normal files one mismatch' +); + +unlink("$output_directory/tmp1.sam"); +unlink("$output_directory/tmp2.sam"); +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + + +# Test pipeline with gzipped input +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +$fastqfile = "t/data/RunTradisBWA/test.tagged.fastq.gz"; +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object with gzipped data - Normal files one mismatch' +); + +ok( $obj->run_tradis, 'testing complete analysis with gzipped data' ); +ok( + -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence (gzipped data) - Normal files one mismatch' +); +ok( -e "$output_directory/test.plot.mapped.bam", 'checking mapped bam existence - Normal files one mismatch'); +ok( -e "$output_directory/test.plot.mapped.bam.bai", 'checking indexed bam file - Normal files one mismatch'); + +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline with gzipped data file contents - Normal files one mismatch' +); + +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + k => 10, + + ), + 'creating object with custom smalt parameters' +); +# Filtering step +$obj->_filter; +$obj->_remove; +ok( $obj->_map, 'mapping with custom parameters fine' ); + + +# Check die if ref is not found +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => "not_really_a_ref.fa", + tag => $tag, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + + ), + 'creating object' +); +throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; + +unlink('t/data/RunTradisBWA/smallref.fa.amb'); +unlink('t/data/RunTradisBWA/smallref.fa.ann'); +unlink('t/data/RunTradisBWA/smallref.fa.bwt'); +unlink('t/data/RunTradisBWA/smallref.fa.pac'); +unlink('t/data/RunTradisBWA/smallref.fa.sa'); +rmtree($output_directory); +done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisSmalt.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisSmalt.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisSmalt.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,269 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use Cwd; +use File::Path 'rmtree'; +use File::Temp; +use Test::Files qw(compare_ok); + +BEGIN { unshift( @INC, './lib' ) } +BEGIN { unshift( @INC, '../lib' ) } + +BEGIN { + use Test::Most; + use Test::Exception; + use_ok('Bio::Tradis::RunTradis'); +} + +my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_smalt_tests_XXXXX', + CLEANUP => 0, + DIR => cwd() ); +my $output_directory = $output_directory_obj->dirname; +my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +my $temp_directory = $temp_directory_obj->dirname(); + +my ( $obj, $fastqfile, $stats_handle, $ref, $tag, $outfile, $aligner); + +# First, test all parts and complete pipeline without mismatch + +$fastqfile = "t/data/RunTradisSmalt/test.tagged.fastq"; +$ref = "t/data/RunTradisSmalt/smallref.fa"; +$tag = "TAAGAGTCAG"; +$outfile = "test.plot"; +$aligner = 1; +open( $stats_handle, '>', "$output_directory/test.stats" ); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files, no mismatch' +); + +# Filtering step +ok( $obj->_filter, 'testing filtering step' ); +ok( + -e "$temp_directory/filter.fastq", + 'checking filtered file existence - Normal files, no mismatch' +); +compare_ok( + "$temp_directory/filter.fastq", + 't/data/RunTradisSmalt/filtered.fastq', + 'checking filtered file contents - Normal files, no mismatch' +); + +# Check filtering step +ok( $obj->_check_filter, 'testing check filtering step' ); +system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads'; +system("touch $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty'; +system("echo foo > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines'; +system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq'; +system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq"); +throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short'; +system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq"); +ok( $obj->_check_filter, 'check very basic filtered reads validation'); +system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq"); + +# Tag removal +ok( $obj->_remove, 'testing tag removal' ); +ok( -e "$temp_directory/tags_removed.fastq", + 'checking de-tagged file existence - Normal files, no mismatch' ); +compare_ok( + "$temp_directory/tags_removed.fastq", + 't/data/RunTradisSmalt/notags.fastq', + 'checking de-tagged file contents - Normal files, no mismatch' +); + +# Mapping +ok( $obj->_map, 'testing mapping' ); +ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' ); +`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`; +`grep -v "\@PG" t/data/RunTradisSmalt/mapped.sam > $output_directory/tmp2.sam`; +compare_ok( + "$output_directory/tmp1.sam", + "$output_directory/tmp2.sam", + 'checking mapped file contents' +); + +# Conversion +ok( $obj->_sam2bam, 'testing SAM/BAM conversion' ); +ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' ); + +# Sorting +ok( $obj->_sort_bam, 'testing BAM sorting' ); +ok( -e "$temp_directory/mapped.sort.bam", + 'checking sorted BAM existence - Normal files, no mismatch' ); +ok( -e "$temp_directory/mapped.sort.bam.bai", + 'checking indexed BAM existence - Normal files, no mismatch' ); + +#Bamcheck +ok( $obj->_bamcheck, 'testing bamcheck' ); +ok( -e "$temp_directory/mapped.bamcheck", + 'checking bamcheck file existence - Normal files, no mismatch' ); + +# Plot +ok( $obj->_make_plot, 'testing plotting' ); +ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system( +"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped" +); +system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking plot file contents - Normal files, no mismatch' +); + + +# Complete pipeline +ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline file contents - Normal files, no mismatch' +); + +unlink("$temp_directory/filter.fastq"); +unlink("$temp_directory/tags_removed.fastq"); + +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + +# Test complete pipeline with 1 mismatch allowed + +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + mismatch => 1, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files one mismatch' +); + +ok( $obj->run_tradis, 'testing complete analysis with mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files one mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system( + "gunzip -c t/data/RunTradisSmalt/expected.1mm.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline with mismatch file contents - Normal files one mismatch' +); + +unlink("$output_directory/tmp1.sam"); +unlink("$output_directory/tmp2.sam"); +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + +# Test pipeline with gzipped input +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +$fastqfile = "t/data/RunTradisSmalt/test.tagged.fastq.gz"; +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object with gzipped data - Normal files one mismatch' +); + +ok( $obj->run_tradis, 'testing complete analysis with gzipped data' ); +ok( + -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence (gzipped data) - Normal files one mismatch' +); +ok( -e "$output_directory/test.plot.mapped.bam", 'checking mapped bam existence - Normal files one mismatch'); +ok( -e "$output_directory/test.plot.mapped.bam.bai", 'checking indexed bam file - Normal files one mismatch'); + +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline with gzipped data file contents - Normal files one mismatch' +); + +# Test mapping stage with custom smalt parameters +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + tag => $tag, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + smalt_k => 10, + smalt_s => 2 + ), + 'creating object with custom smalt parameters' +); +# Filtering step +$obj->_filter; +$obj->_remove; +ok( $obj->_map, 'mapping with custom parameters fine' ); + +# Check die if ref is not found +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => "not_really_a_ref.fa", + tag => $tag, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + smalt_k => 10, + smalt_s => 2 + ), + 'creating object with custom smalt parameters' +); +throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; + +rmtree($output_directory); +done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradis.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradis.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradis.t 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradis.t 1970-01-01 00:00:00.000000000 +0000 @@ -1,264 +0,0 @@ -#!/usr/bin/env perl -use strict; -use warnings; -use Cwd; -use File::Path 'rmtree'; -use File::Temp; -use Test::Files qw(compare_ok); - -BEGIN { unshift( @INC, './lib' ) } -BEGIN { unshift( @INC, '../lib' ) } - -BEGIN { - use Test::Most; - use Test::Exception; - use_ok('Bio::Tradis::RunTradis'); -} - -my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_tests_XXXXX', - CLEANUP => 0, - DIR => cwd() ); -my $output_directory = $output_directory_obj->dirname; -my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0, - DIR => $output_directory ); -my $temp_directory = $temp_directory_obj->dirname(); - -my ( $obj, $fastqfile, $stats_handle, $ref, $tag, $outfile ); - -# First, test all parts and complete pipeline without mismatch - -$fastqfile = "t/data/RunTradis/test.tagged.fastq"; -$ref = "t/data/RunTradis/smallref.fa"; -$tag = "TAAGAGTCAG"; -$outfile = "test.plot"; -open( $stats_handle, '>', "$output_directory/test.stats" ); - -ok( - $obj = Bio::Tradis::RunTradis->new( - fastqfile => $fastqfile, - reference => $ref, - tag => $tag, - outfile => $outfile, - output_directory => $output_directory, - _temp_directory => $temp_directory, - _stats_handle => $stats_handle - ), - 'creating object - Normal files, no mismatch' -); - -# Filtering step -ok( $obj->_filter, 'testing filtering step' ); -ok( - -e "$temp_directory/filter.fastq", - 'checking filtered file existence - Normal files, no mismatch' -); -compare_ok( - "$temp_directory/filter.fastq", - 't/data/RunTradis/filtered.fastq', - 'checking filtered file contents - Normal files, no mismatch' -); - -# Check filtering step -ok( $obj->_check_filter, 'testing check filtering step' ); -system("mv $temp_directory/filter.fastq $temp_directory/filter.fastq.bak"); -throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if no filtered reads'; -system("touch $temp_directory/filter.fastq"); -throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are empty'; -system("echo foo > $temp_directory/filter.fastq"); -throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads has less than 4 lines'; -system("echo 'foo\nbar\nbaz\nquux' > $temp_directory/filter.fastq"); -throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads do not look like a fastq'; -system("echo 'foo\nbar\n+' > $temp_directory/filter.fastq"); -throws_ok {$obj->_check_filter} 'Bio::Tradis::Exception::TagFilterError', 'complain if filtered reads are too short'; -system("echo 'foo\nbar\n+\nquux' > $temp_directory/filter.fastq"); -ok( $obj->_check_filter, 'check very basic filtered reads validation'); -system("mv $temp_directory/filter.fastq.bak $temp_directory/filter.fastq"); - -# Tag removal -ok( $obj->_remove, 'testing tag removal' ); -ok( -e "$temp_directory/tags_removed.fastq", - 'checking de-tagged file existence - Normal files, no mismatch' ); -compare_ok( - "$temp_directory/tags_removed.fastq", - 't/data/RunTradis/notags.fastq', - 'checking de-tagged file contents - Normal files, no mismatch' -); - -# Mapping -ok( $obj->_map, 'testing mapping' ); -ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' ); -`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`; -`grep -v "\@PG" t/data/RunTradis/mapped.sam > $output_directory/tmp2.sam`; -compare_ok( - "$output_directory/tmp1.sam", - "$output_directory/tmp2.sam", - 'checking mapped file contents' -); - -# Conversion -ok( $obj->_sam2bam, 'testing SAM/BAM conversion' ); -ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' ); - -# Sorting -ok( $obj->_sort_bam, 'testing BAM sorting' ); -ok( -e "$temp_directory/mapped.sort.bam", - 'checking sorted BAM existence - Normal files, no mismatch' ); -ok( -e "$temp_directory/mapped.sort.bam.bai", - 'checking indexed BAM existence - Normal files, no mismatch' ); - -#Bamcheck -ok( $obj->_bamcheck, 'testing bamcheck' ); -ok( -e "$temp_directory/mapped.bamcheck", - 'checking bamcheck file existence - Normal files, no mismatch' ); - -# Plot -ok( $obj->_make_plot, 'testing plotting' ); -ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz", - 'checking plot file existence - Normal files, no mismatch' ); -system( -"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped" -); -system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped"); -compare_ok( - "$output_directory/test.plot.unzipped", - "$output_directory/expected.plot.unzipped", - 'checking plot file contents - Normal files, no mismatch' -); - - -# Complete pipeline -ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' ); -ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", - 'checking plot file existence - Normal files, no mismatch' ); -system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); -system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped"); -compare_ok( - "$output_directory/test.plot.unzipped", - "$output_directory/expected.plot.unzipped", - 'checking completed pipeline file contents - Normal files, no mismatch' -); - -unlink("$temp_directory/filter.fastq"); -unlink("$temp_directory/tags_removed.fastq"); - -unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); -unlink("$output_directory/expected.plot.unzipped"); -unlink("$output_directory/test.plot.unzipped"); - -# Test complete pipeline with 1 mismatch allowed - -$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, - DIR => $output_directory ); -$temp_directory = $temp_directory_obj->dirname(); - -ok( - $obj = Bio::Tradis::RunTradis->new( - fastqfile => $fastqfile, - reference => $ref, - tag => $tag, - outfile => $outfile, - mismatch => 1, - output_directory => $output_directory, - _temp_directory => $temp_directory, - _stats_handle => $stats_handle - ), - 'creating object - Normal files one mismatch' -); - -ok( $obj->run_tradis, 'testing complete analysis with mismatch' ); -ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", - 'checking plot file existence - Normal files one mismatch' ); -system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); -system( - "gunzip -c t/data/RunTradis/expected.1mm.plot.gz > $output_directory/expected.plot.unzipped"); -compare_ok( - "$output_directory/test.plot.unzipped", - "$output_directory/expected.plot.unzipped", - 'checking completed pipeline with mismatch file contents - Normal files one mismatch' -); - -unlink("$output_directory/tmp1.sam"); -unlink("$output_directory/tmp2.sam"); -unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); -unlink("$output_directory/expected.plot.unzipped"); -unlink("$output_directory/test.plot.unzipped"); - -# Test pipeline with gzipped input -$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, - DIR => $output_directory ); -$temp_directory = $temp_directory_obj->dirname(); -$fastqfile = "t/data/RunTradis/test.tagged.fastq.gz"; -ok( - $obj = Bio::Tradis::RunTradis->new( - fastqfile => $fastqfile, - reference => $ref, - tag => $tag, - outfile => $outfile, - output_directory => $output_directory, - _temp_directory => $temp_directory, - _stats_handle => $stats_handle - ), - 'creating object with gzipped data - Normal files one mismatch' -); - -ok( $obj->run_tradis, 'testing complete analysis with gzipped data' ); -ok( - -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", - 'checking plot file existence (gzipped data) - Normal files one mismatch' -); -ok( -e "$output_directory/test.plot.mapped.bam", 'checking mapped bam existence - Normal files one mismatch'); -ok( -e "$output_directory/test.plot.mapped.bam.bai", 'checking indexed bam file - Normal files one mismatch'); - -system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); -system("gunzip -c t/data/RunTradis/expected.plot.gz > $output_directory/expected.plot.unzipped"); -compare_ok( - "$output_directory/test.plot.unzipped", - "$output_directory/expected.plot.unzipped", - 'checking completed pipeline with gzipped data file contents - Normal files one mismatch' -); - -# Test mapping stage with custom smalt parameters -$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, - DIR => $output_directory ); -$temp_directory = $temp_directory_obj->dirname(); -ok( - $obj = Bio::Tradis::RunTradis->new( - fastqfile => $fastqfile, - reference => $ref, - tag => $tag, - outfile => $outfile, - output_directory => $output_directory, - _temp_directory => $temp_directory, - _stats_handle => $stats_handle, - smalt_k => 10, - smalt_s => 2 - ), - 'creating object with custom smalt parameters' -); -# Filtering step -$obj->_filter; -$obj->_remove; -ok( $obj->_map, 'mapping with custom parameters fine' ); - -# Check die if ref is not found -$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, - DIR => $output_directory ); -$temp_directory = $temp_directory_obj->dirname(); -ok( - $obj = Bio::Tradis::RunTradis->new( - fastqfile => $fastqfile, - reference => "not_really_a_ref.fa", - tag => $tag, - outfile => $outfile, - output_directory => $output_directory, - _temp_directory => $temp_directory, - _stats_handle => $stats_handle, - smalt_k => 10, - smalt_s => 2 - ), - 'creating object with custom smalt parameters' -); -throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; - -rmtree($output_directory); -done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisTaglessBwa.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisTaglessBwa.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessBwa.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,156 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use Cwd; +use File::Path 'rmtree'; +use File::Temp; +use Test::Files qw(compare_ok); + +BEGIN { unshift( @INC, './lib' ) } +BEGIN { unshift( @INC, '../lib' ) } + +BEGIN { + use Test::Most; + use Test::Exception; + use_ok('Bio::Tradis::RunTradis'); +} + +my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_tagless_tests_XXXXX', + CLEANUP => 0, + DIR => cwd() ); +my $output_directory = $output_directory_obj->dirname; +my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +my $temp_directory = $temp_directory_obj->dirname(); + +my ( $obj, $fastqfile, $stats_handle, $ref, $outfile, $aligner); + +# First, test all parts and complete pipeline without mismatch + +$fastqfile = "t/data/RunTradisTaglessBWA/notags.fastq"; +$ref = "t/data/RunTradisTaglessBWA/smallref.fa"; +$outfile = "test.plot"; +$aligner = 0; +open( $stats_handle, '>', "$output_directory/test.stats" ); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files, no mismatch' +); + + + +# Mapping +ok( $obj->_map, 'testing mapping' ); +ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' ); +`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`; +`grep -v "\@PG" t/data/RunTradisTaglessBWA/mapped.sam > $output_directory/tmp2.sam`; +compare_ok( + "$output_directory/tmp1.sam", + "$output_directory/tmp2.sam", + 'checking mapped file contents' +); + +# Conversion +ok( $obj->_sam2bam, 'testing SAM/BAM conversion' ); +ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' ); + +# Sorting +ok( $obj->_sort_bam, 'testing BAM sorting' ); +ok( -e "$temp_directory/mapped.sort.bam", + 'checking sorted BAM existence - Normal files, no mismatch' ); +ok( -e "$temp_directory/mapped.sort.bam.bai", + 'checking indexed BAM existence - Normal files, no mismatch' ); + +#Bamcheck +ok( $obj->_bamcheck, 'testing bamcheck' ); +ok( -e "$temp_directory/mapped.bamcheck", + 'checking bamcheck file existence - Normal files, no mismatch' ); + +# Plot +ok( $obj->_make_plot, 'testing plotting' ); +ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system( +"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped" +); +system("gunzip -c t/data/RunTradisTaglessBWA/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking plot file contents - Normal files, no mismatch' +); + + +# Complete pipeline +ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisTaglessBWA/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline file contents - Normal files, no mismatch' +); + +unlink("$temp_directory/filter.fastq"); +unlink("$temp_directory/tags_removed.fastq"); + +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + k => 10, + + ), + 'creating object with custom smalt parameters' +); + +ok( $obj->_map, 'mapping with custom parameters fine' ); + +# Check die if ref is not found +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => "not_really_a_ref.fa", + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + + ), + 'creating object' +); +throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; + +unlink('t/data/RunTradisTaglessBWA/smallref.fa.amb'); +unlink('t/data/RunTradisTaglessBWA/smallref.fa.ann'); +unlink('t/data/RunTradisTaglessBWA/smallref.fa.bwt'); +unlink('t/data/RunTradisTaglessBWA/smallref.fa.pac'); +unlink('t/data/RunTradisTaglessBWA/smallref.fa.sa'); +rmtree($output_directory); +done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisTaglessSmalt.t bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t --- bio-tradis-1.4.1+dfsg/t/Bio/Tradis/RunTradisTaglessSmalt.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/Bio/Tradis/RunTradisTaglessSmalt.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,154 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use Cwd; +use File::Path 'rmtree'; +use File::Temp; +use Test::Files qw(compare_ok); + +BEGIN { unshift( @INC, './lib' ) } +BEGIN { unshift( @INC, '../lib' ) } + +BEGIN { + use Test::Most; + use Test::Exception; + use_ok('Bio::Tradis::RunTradis'); +} + +my $output_directory_obj = File::Temp->newdir( 'tmp_run_tradis_tagless_smalt_tests_XXXXX', + CLEANUP => 0, + DIR => cwd() ); +my $output_directory = $output_directory_obj->dirname; +my $temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +my $temp_directory = $temp_directory_obj->dirname(); + +my ( $obj, $fastqfile, $stats_handle, $ref, $outfile, $aligner); + +# First, test all parts and complete pipeline without mismatch + +$fastqfile = "t/data/RunTradisTaglessSmalt/notags.fastq"; +$ref = "t/data/RunTradisTaglessSmalt/smallref.fa"; +$outfile = "test.plot"; +$aligner = 1; +open( $stats_handle, '>', "$output_directory/test.stats" ); + +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle + ), + 'creating object - Normal files, no mismatch' +); + + + +# Mapping +ok( $obj->_map, 'testing mapping' ); +ok( -e "$temp_directory/mapped.sam", 'checking SAM existence' ); +`grep -v "\@PG" $temp_directory/mapped.sam > $output_directory/tmp1.sam`; +`grep -v "\@PG" t/data/RunTradisTaglessSmalt/mapped.sam > $output_directory/tmp2.sam`; +compare_ok( + "$output_directory/tmp1.sam", + "$output_directory/tmp2.sam", + 'checking mapped file contents' +); + +# Conversion +ok( $obj->_sam2bam, 'testing SAM/BAM conversion' ); +ok( -e "$temp_directory/mapped.bam", 'checking BAM existence' ); + +# Sorting +ok( $obj->_sort_bam, 'testing BAM sorting' ); +ok( -e "$temp_directory/mapped.sort.bam", + 'checking sorted BAM existence - Normal files, no mismatch' ); +ok( -e "$temp_directory/mapped.sort.bam.bai", + 'checking indexed BAM existence - Normal files, no mismatch' ); + +#Bamcheck +ok( $obj->_bamcheck, 'testing bamcheck' ); +ok( -e "$temp_directory/mapped.bamcheck", + 'checking bamcheck file existence - Normal files, no mismatch' ); + +# Plot +ok( $obj->_make_plot, 'testing plotting' ); +ok( -e "$temp_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system( +"gunzip -c $temp_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped" +); +system("gunzip -c t/data/RunTradisTaglessSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking plot file contents - Normal files, no mismatch' +); + + +# Complete pipeline +ok( $obj->run_tradis, 'testing complete analysis - Normal files, no mismatch' ); +ok( -e "$output_directory/test.plot.AE004091.insert_site_plot.gz", + 'checking plot file existence - Normal files, no mismatch' ); +system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped"); +system("gunzip -c t/data/RunTradisTaglessSmalt/expected.plot.gz > $output_directory/expected.plot.unzipped"); +compare_ok( + "$output_directory/test.plot.unzipped", + "$output_directory/expected.plot.unzipped", + 'checking completed pipeline file contents - Normal files, no mismatch' +); + + + +unlink("$output_directory/test.plot.AE004091.insert_site_plot.gz"); +unlink("$output_directory/expected.plot.unzipped"); +unlink("$output_directory/test.plot.unzipped"); + + + +# Test mapping stage with custom smalt parameters +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => $ref, + smalt => $aligner, + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + smalt_k => 10, + smalt_s => 2 + ), + 'creating object with custom smalt parameters' +); + +ok( $obj->_map, 'mapping with custom parameters fine' ); + +# Check die if ref is not found +$temp_directory_obj = File::Temp->newdir( CLEANUP => 0, + DIR => $output_directory ); +$temp_directory = $temp_directory_obj->dirname(); +ok( + $obj = Bio::Tradis::RunTradis->new( + fastqfile => $fastqfile, + reference => "not_really_a_ref.fa", + outfile => $outfile, + output_directory => $output_directory, + _temp_directory => $temp_directory, + _stats_handle => $stats_handle, + smalt_k => 10, + smalt_s => 2 + ), + 'creating object with custom smalt parameters' +); +throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; + +rmtree($output_directory); +done_testing(); diff -Nru bio-tradis-1.4.1+dfsg/t/data/Map/expected.bwa.mapped bio-tradis-1.4.5+dfsg2/t/data/Map/expected.bwa.mapped --- bio-tradis-1.4.1+dfsg/t/data/Map/expected.bwa.mapped 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/Map/expected.bwa.mapped 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,25 @@ +@SQ SN:AE004091 LN:9840 +@PG ID:bwa PN:bwa VN:0.7.17-r1194-dirty CL:bwa mem -k 13 -t 4 smallref.fa test.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7058 60 44M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 MD:Z:38 AS:i:38 XS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 60 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 MD:Z:42 AS:i:42 XS:i:0 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 60 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:2 MD:Z:0G11T31 AS:i:38 XS:i:0 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3184 60 44M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:1 MD:Z:0G43 AS:i:43 XS:i:0 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3957 60 44M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:1 MD:Z:0T43 AS:i:43 XS:i:0 diff -Nru bio-tradis-1.4.1+dfsg/t/data/Map/expected.mapped bio-tradis-1.4.5+dfsg2/t/data/Map/expected.mapped --- bio-tradis-1.4.1+dfsg/t/data/Map/expected.mapped 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/Map/expected.mapped 1970-01-01 00:00:00.000000000 +0000 @@ -1,26 +0,0 @@ -@HD VN:1.3 SO:unknown -@SQ SN:AE004091 LN:9840 -@PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 test.ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/Map/test.fastq -HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43 -HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43 -HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43 -HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43 -HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43 -HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43 -HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0 -HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42 -HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40 -HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43 -HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43 diff -Nru bio-tradis-1.4.1+dfsg/t/data/Map/expected.smalt.mapped bio-tradis-1.4.5+dfsg2/t/data/Map/expected.smalt.mapped --- bio-tradis-1.4.1+dfsg/t/data/Map/expected.smalt.mapped 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/Map/expected.smalt.mapped 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,26 @@ +@HD VN:1.3 SO:unknown +@SQ SN:AE004091 LN:9840 +@PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 test.ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/Map/test.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43 Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradis/expected.1mm.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradis/expected.1mm.plot.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradis/expected.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradis/expected.plot.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/filelist.txt bio-tradis-1.4.5+dfsg2/t/data/RunTradis/filelist.txt --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/filelist.txt 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/filelist.txt 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -test.tagged.fastq -test2.tagged.fastq diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/filtered.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradis/filtered.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/filtered.fastq 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/filtered.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,92 +0,0 @@ -@HS21_09876:1:1105:9650:48712#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF -@HS21_09876:1:1106:8638:38957#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD -@HS21_09876:1:1204:19746:42237#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF -@HS21_09876:1:2210:2408:11148#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE -@HS21_09876:1:1201:6607:66324#83 -TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD -@HS21_09876:1:2102:12312:75235#83 -TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE -@HS21_09876:1:1106:16061:54950#83 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD -@HS21_09876:1:2207:12005:97464#83 -TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG -+ -BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D -@HS21_09876:1:1208:12319:4648#83 -TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC -+ -B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF -@HS21_09876:2:1211:5990:82312#83 -TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC -+ -BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE -@HS21_09876:2:2103:19946:55809#83 -TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC -+ -BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/mapped.sam bio-tradis-1.4.5+dfsg2/t/data/RunTradis/mapped.sam --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/mapped.sam 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/mapped.sam 1970-01-01 00:00:00.000000000 +0000 @@ -1,26 +0,0 @@ -@HD VN:1.3 SO:unknown -@SQ SN:AE004091 LN:9840 -@PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/RunTradis/notags.fastq -HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43 -HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43 -HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43 -HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43 -HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43 -HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43 -HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0 -HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42 -HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40 -HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43 -HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43 diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/notags.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradis/notags.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/notags.fastq 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/notags.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,92 +0,0 @@ -@HS21_09876:1:1105:9650:48712#83 -GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF -@HS21_09876:1:1106:8638:38957#83 -GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD -@HS21_09876:1:1204:19746:42237#83 -GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF -@HS21_09876:1:2210:2408:11148#83 -GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE -@HS21_09876:1:1201:6607:66324#83 -CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD -@HS21_09876:1:2102:12312:75235#83 -CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE -@HS21_09876:1:1106:16061:54950#83 -GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD -@HS21_09876:1:2207:12005:97464#83 -GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG -+ -HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D -@HS21_09876:1:1208:12319:4648#83 -CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC -+ -AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF -@HS21_09876:2:1211:5990:82312#83 -TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC -+ -HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE -@HS21_09876:2:2103:19946:55809#83 -GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC -+ -HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/smallref.fa bio-tradis-1.4.5+dfsg2/t/data/RunTradis/smallref.fa --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/smallref.fa 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/smallref.fa 1970-01-01 00:00:00.000000000 +0000 @@ -1,165 +0,0 @@ ->AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome. -tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat -gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc -tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc -ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg -gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta -cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc -ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc -ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat -ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc -aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg -tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc -tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca -gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc -cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag -tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg -agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg -cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca -accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg -ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg -gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga -acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg -ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt -tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca -ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga -aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg -ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg -cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg -tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc -cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc -tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg -atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc -tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg -atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg -atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag -gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa -ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg -gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt -cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg -atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag -aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat -ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg -cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc -aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac -cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc -gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc -ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg -aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag -ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc -aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg -aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac -ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag -caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat -gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc -cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc -atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac -ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag -gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg -gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg -agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg -ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg -gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc -tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc -ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta -ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga -ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag -cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt -cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc -atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac -gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat -ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc -acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc -atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga -aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca -ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg -gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca -atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga -tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg -gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca -tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac -tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg -agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt -ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc -tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg -cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag -tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc -cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga -acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg -atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct -cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg -gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca -agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc -gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg -acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc -agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg -aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc -tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca -tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct -tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt -tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag -agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg -gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc -tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta -ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc -aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag -accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct -acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg -gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc -gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc -acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca -ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg -accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa -gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg -aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca -ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac -ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc -gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc -ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca -cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat -ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc -gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca -gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc -gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg -cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt -ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag -ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag -tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat -cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac -cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc -gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc -ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga -ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct -ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa -tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac -agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag -tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc -tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag -ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg -cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa -tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc -gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc -ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg -aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt -gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc -acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg -ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt -tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc -atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac -cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg -cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg -gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg -acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac -ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga -ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat -ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat -cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg -gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg -attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg -gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc -ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc -aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg -ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac -aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc -gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac -gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/test2.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test2.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/test2.tagged.fastq 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test2.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,452 +0,0 @@ -@HS21_09876:1:1207:4978:63940#75 -TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC -+ -CCCFFFFFHHGHC7E4EEFGFFGGFFFCEG@EHGFFEGFEGFFEGEHFFGFGFE -@HS21_09876:1:1203:13201:16985#75 -TAAGAGTCAGCGGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGA -+ -BCCFFFFFGHHHCED9GEFDEFGFIFEGCEFEHGGFGGFFGFFGGEFGHGEGFF -@HS21_09876:1:1105:14817:70208#75 -TAAGAGTCAGGCCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGACGAAGCCC -+ -CCCFFFFFHHHHCEF8HHFGCFGGEFEFEGGEFFGFFGFFGFGFGEGGHGFEFE -@HS21_09876:1:1101:1155:30938#75 -TAAGAGTCAGGTTGCATAACTCGACGAAGCCCAGCAACTGCGTGTTTCTCCGGC -+ -B=?DDDEFHCFHBDD,AEFEGDGGCFFGE>DEAHEFFFCFGFFFDEGEFGFFFE -@HS21_09876:1:2204:6930:62477#75 -TAAGAGTCAGGGGCAAAAGGTTGTCGAGAACCGGTGTCGAGGCTGTTTCCTTCC -+ -BBCFFFFFHHHHCEF5GHFFCFDGEFBCHFFEFFGFFGFFGFFDGEEGFGFGFE -@HS21_09876:1:2211:14592:36752#75 -TAAGAGTCAGGGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTCCCCC -+ -CCCFFFFFHFHH9BF%GGFFEFDGFFF;EFFEHGGFEGFFGFFEGDEFHGFGFE -@HS21_09876:1:1101:1117:56616#75 -TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC -+ -=:=DADDDFFHHCDF8EEFGGFGEEFDGHEEEGGCFFFFFGFGFGCGGFGE@ED -@HS21_09876:1:1106:9993:12675#75 -TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC -+ -BBBFFFFFHHFHCBI2DEFGGFGEFFFGHGIEHHGFFGFFGFFJGEHFFGFDFE -@HS21_09876:1:2205:12308:83747#75 -TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC -+ -BCCFFFFFHHHHC@F7EEFGFFGFEFGGGFHEGEFFFGFFGFFECDEGHGFFFF -@HS21_09876:1:2211:5325:48675#75 -TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC -+ -1:B4A2AD2ACF57<'GE4EEFG9@FDDGGIEE?F:=8FEGFGDGACGFGEDA: -@HS21_09876:1:1202:13852:46659#75 -TAAGAGTCAGGGGCCAACGGCATCGCCAGCAACCTGGGGATTTCCCGTGAGCGC -+ -CCCFFFFFHHHHCEH8EEFGFFDG7FG;EFFEAHEFGGFFBFGEGEGGFGEGFF -@HS21_09876:1:1110:4160:49896#75 -TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG -+ -BCBFFFFDHHHHCDF8AEFGCFGHDFGCHGDEFFGFFGGFGFGFG8GGHGFFFE -@HS21_09876:1:2205:9754:20814#75 -TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG -+ -BBCFDEFEHHHHCEE4EIFGGFAFEFGGHFFEGEFFGGFEGFFFGEFEHGFEFF -@HS21_09876:1:1104:13063:60859#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHH>0@F,GEFE3CHEEFDC2FEEAG?FCEFED=F8CEEEH;;EDE -@HS21_09876:1:1107:8692:25384#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -@@CFFFFFHHHHA@E7EIFEEFGE-F@EHDCFF8G>GFFBGCCCHGF:AD -@HS21_09876:1:1109:11137:7630#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BCCFFFFFHHGHCBF8EEFDEFGEEFGG>GFEGGCFFGGFGFFEGGFFHGFEFF -@HS21_09876:1:1110:7663:40978#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BB@=DADDHDFH?7D9EGFFEFGFEFF;>FDED?FFEGGEGFGFACFFFGFFFE -@HS21_09876:1:1201:5332:2719#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BCCFFFFFHHHHADF4EHFEEFGFEFEGCG@EEFCFFGFFGFGFGEEGHGFFFD -@HS21_09876:1:1204:12364:36595#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCBD2EGFFFFEDFEFFGFFGFGEGEGEHGFGFF -@HS21_09876:1:2102:4320:20528#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBBFFFDDFFHHCEF2EEFGCFGEEGED>G@EEGEFGGGEGFGEBCEGHGFEED -@HS21_09876:1:2102:17907:93005#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCEE5EEFFEFGEEFEGFEEEDFCFGGFFGFFGGGFGHGFEFF -@HS21_09876:1:2104:19430:56353#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCDFFFEHHHHCBH5FGFEEFGEDEFG>EHEEEEFFGGEGFFEGDGGFGFGFE -@HS21_09876:1:2106:8768:77924#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHCBE7EGFFEFG87CEDFEFEFHCFFGFFGFFEGEGEHGFEDF -@HS21_09876:1:2109:3560:75405#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -B@@DFDDFHHHHCBD,FGFEFIEGGFFGGGFGFFEGEFGFGFEFD -@HS21_09876:1:2201:7109:15683#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHCBF5GHFECFGEFFEGEGEEEFFFEGFFGFFGGGEFHGFEFF -@HS21_09876:1:2204:5779:59154#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFEHHHHCEF7EEFFE@EHGFFFGGEGFFDCEEGHGEFFE -@HS21_09876:1:2210:14908:13619#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHFHHC7H,EEFGDEEAFGF=GA>GFG8GCGGHGFDFD -@HS21_09876:1:2210:1263:58662#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBBFFFFFHHHGBBH4HE?FE@GC7GFDFEDEAHCFFG;>GFGFG8EEHGF@DD -@HS21_09876:1:2211:14421:77160#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHFFF;EE-HEFFCFGCDFGDFFHEDFFFGGFEGFGEGEGGHGFGEF -@HS21_09876:1:1107:18833:61679#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -CCCFFFFFHHHH87E,G24E<9IE-FGFFG/1GFFFGEGE=;FGFC -@HS21_09876:1:1201:13166:59616#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -BCCFFFFFHHHHCDF5GEFFEFEFEFFDEGGEHGEFEEFFGFGFGDEGHGFGFD -@HS21_09876:1:1205:1312:68078#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -B@@FFFFFHHHHCDE,GEFCEFEFEFDGCGFEGGGFFEFEGFFEGECEHGFFFE -@HS21_09876:1:2101:9743:73722#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -BCCFFFFFHHHHCDF7EEFFEFGFEFBDFEHEEFGFFFFFGFGFGEEEFGFEFE -@HS21_09876:1:2112:4406:21609#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -BBCDFFFFHHHD-<<+8=FHEGFGGFEGFE?GDGG=GDFBE -@HS21_09876:1:2207:5093:25809#75 -TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC -+ -BBCDDEFDHHFFCBF,FEFECFGFFFF;HGGEFFEFEGFFGFGDGEGGHGFFBE -@HS21_09876:1:1105:3593:46102#75 -TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC -+ -CCCFFFFFHHHHCDE4EGFGECGFEFFEGFEEGFEFEGGEGFFJGFFGHGFGFF -@HS21_09876:1:1214:11162:39342#75 -TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC -+ -BCCDDFFFHHHHCB<&3GFEFFGGEFFDFGDEHGECGGGFGFFFGEEGFDFEFD -@HS21_09876:1:2103:18144:97839#75 -TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC -+ -CCCFFFFFHHGFCEE'EIFFGFDFDFECGGHEFGGFFCGFGFGDGEGEHGFEFD -@HS21_09876:1:1109:10864:56828#75 -TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC -+ -BCCDFFFFHHHFABE2EHFGCFEEEDFEAF?FEGAD==GE98EG=G@@ED -@HS21_09876:1:2108:6881:4925#75 -TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA -+ -CCCFFFEEHHHHCEE0EEFGFFGGEFDGHEFEEFGFGFGFGFGDGDEEHGDEFE -@HS21_09876:1:1111:18499:9859#75 -TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC -+ -BBCFFFFFHHHHCEF0GEFDEFEFIFFGGGFEHDGFFGGFGFFEGEGFHGFGFF -@HS21_09876:1:1210:19511:97335#75 -TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC -+ -CCCFFFFDHFFHCDH7HGFGGFGEIFFGHGHEFFGFFGFEGFFGGGGEHGFEFD -@HS21_09876:1:1103:13218:78186#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -CCCFFFFFHHHHCDF7EEFDC9GEFFECEEFEHGGFGGFFGFFFGGFGFGFFFC -@HS21_09876:1:2107:11891:7630#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -@CCFFDDDHFFHCED0GIFDEFGEEFFDEFIEEFEFFEFEGFFBGEFGFGFEFD -@HS21_09876:1:2201:9833:67072#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -CCCFFFFFHHHHCEE5GHFDEFGHDFEDFEGEEHGFGGFFGFGFGDGGFGFEFC -@HS21_09876:2:2101:20921:89053#75 -TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC -+ -CCCFFFFFHHHHD9E0FEFEGGGFHFFHHGGFGCFGFHFFGGGFFFFFGFEEEF -@HS21_09876:2:2205:9713:92092#75 -TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC -+ -CCCFFFFFHHHGED<6?EFEDG;:EEC;=GEAG@GFF;FGGCA9F>DFDFCE@E -@HS21_09876:2:2208:11577:65116#75 -TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC -+ -BBCFFDFFDFFA@AE3F3@D:GGFD:FHD>=FGFGD1GDAGF?FEGGDEFGFFGDG9FFFFFCG;AFFFFFGFEF9E -@HS21_09876:2:2103:7357:48165#75 -TAAGAGTCAGCCCATCCACCTGCTGGGCCTGGCGCGTTCATTCCGCAGTGCGCG -+ -CCCFFFFFHHHHDEE3GEDFGGGFEGGFHGFFGGGEFHFFGGGFFFFFDFHFEF -@HS21_09876:2:1102:4592:99056#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHDDE,FFGFFGGF-GIFCFGFGHDDFGFFGGEFFFFFEFFFED -@HS21_09876:2:1105:18701:63246#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHFDE3FFFEFGGDDFFFDEHEGHGFFFFF>GFFFFFFGFEFED -@HS21_09876:2:1107:9181:47786#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHFHHEDE1FFF4GGGEEFGFFGFHGHGFFHFFGEGFFFEFEFEFCE -@HS21_09876:2:2101:7072:68459#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHDEE3FFFFDGGF7EFHAFFGGFGEFHFFGGGFFFFFGFHFFD -@HS21_09876:2:2104:11024:92879#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHDDE7FFDG:GGDEEFF=GGFAHFFFFFGGEEFFFFFGFEFEF -@HS21_09876:2:2106:9334:51625#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BB@FBDADFHHFEA<1FFG::=GFH0=;1>=FA@D>FAF<>;A9FFFFG?=B9E -@HS21_09876:2:2107:14640:85151#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BB@BDDFFHHFHFEE,FIDFDGGDFFGF=GHGGHFFFHFHGEGFFF@FGEEEDD -@HS21_09876:2:2201:18727:56295#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -B=BDFFFFHHD>EAE3GDFCD=GEEDGH1>C6GGD>FG3FGHEFFF0F7EEDDC -@HS21_09876:2:2203:20492:60041#75 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFEHFFFCEE'FFFFDGGEEGGFAFFFGHGDFHFFGHGFFFFFGEEEEF -@HS21_09876:2:1102:1602:23426#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BBCFFFFFHHFHDAE6FFDEGGGDC:FDHEGHA@GGFGFFGEGFFFFFGEFBFE -@HS21_09876:2:1104:6936:48990#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -CCCFFFFFHHHHDEE,FFFEGGGDF:F;HFGFGFGEFGFFGGEGFFFFGFFFEF -@HS21_09876:2:2101:9813:71457#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BCCDFFFFHHHHEEE3FIDEGGGDEDFAHGGGGGGGFFFFGHEFFFFFEFHDEF -@HS21_09876:2:2201:13960:2115#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BCCFFFFFHHHHFEE4FFGEGGGDFAGDHGHGGGGFFGFFGEDFFFFFDFHDED -@HS21_09876:2:2202:14819:44089#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -CCCFFFFFHHHHD9E4GFFFIGGDF:GDHGGGGHGFFFFFGEEGFFFFEFEEEG -@HS21_09876:2:2203:10287:44498#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BCCFFFFFHHHHDEE6GIFEGGGDDDGHHGGFGFGFFFFEGFFGFFFFGFEEEF -@HS21_09876:2:2206:9622:55348#75 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BBCFFFFFHHHHDDE,FFFEGGGDFAGHHGGFGHFDFFFFGGDFFFFFDEHEEE -@HS21_09876:2:1101:1182:4708#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -BBBFFFFFHHGHF=E6EFFEEGGGFDGGEGFAGFGFFCFFGHEFFFEFFGFEED -@HS21_09876:2:2207:16105:64688#75 -TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC -+ -BCCFFFFFHHHHFEE1FFDDDGBFEGCFAFFEGHDEFCFEGDF9F;@EFGG:EEFH=FCEG3FF<;FFGHFFFFDFGECEDF -@HS21_09876:2:1212:2848:49763#75 -TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG -+ -BCCDDEFFHGGHFDE,DDEDHG;E;FG;HFGEGFGDFF3FGEGFFFFF7FFF9D -@HS21_09876:2:2101:18079:59533#75 -TAAGAGTCAGCCCGTGAAACGCCTGAAAAAGACACTGCACCTTTCAAGCTTGTC -+ -@@@DDDDDHHA+9AB1F>G01AG:CD1H=>CEA3F3FA>FAFEGEGFFFEFGFEEEE -@HS21_09876:2:1111:18613:97316#75 -TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC -+ -BBCBDFFFHHHHDAE,EFFFGGGEEEGADEHFGCGDFGFFGGGFFFFFDGEFCE -@HS21_09876:2:2112:7311:2729#75 -TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC -+ -BCCDFEFEHFFH7EE)GEGFFGGGCEI;HGGFGFGFFHFEGEG6FFDFECC76D -@HS21_09876:2:2209:5184:70364#75 -TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC -+ -CCCFFFFFHFFHDEE7FFFGFGGGDGGHHGGFGFGDFCFFGEEGFFFFEFFFEF -@HS21_09876:2:2206:10363:37150#75 -TAAGAGTCAGGGGGCTTCACCGTAGCCGGCACGGGCGCCCGGCAGATGGTCGGC -+ -BBBFFFFFHHHHDDE1FF@HIGGE?GGFHFEFGHGEFFFFGFGFFFFFGEEFBE -@HS21_09876:2:1211:8018:71514#75 -TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC -+ -BBCDDEDFHHGHDAE,FEDE:2;ECF=H=>GF5@G>FGFH3CGFFF@FDEEF9E -@HS21_09876:2:2207:12305:87719#75 -TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC -+ -@@CADAADFFFFFEE6FEGFGGGFEFFHHGGFGHGFFHFEGHEFFFEFGFEDEB -@HS21_09876:2:1109:4620:60950#75 -TAAGAGTCAGAAAGCAGATCCTCGGGGCCAATCCGCCTCCCGGTGCGCGCGACG -+ -CCCFFFFFHHHHDEE4FFFEGGGHFGGFHFCFGFGEFHFFGGEGFFFFDFEFCE -@HS21_09876:2:1108:17674:57476#75 -TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA -+ -CCCFFFFFHHHHFEE4FFDGIGGGFGGFHGGFGGGFFFFFGFFFFFFFDFHFEC -@HS21_09876:2:1208:4027:38154#75 -TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA -+ -BCCFFFFFHHHHFEE6GFFEIGGGCGFFHGGFGGGEFGFFGFGFFFFFDFHFFE -@HS21_09876:2:2104:21108:77778#75 -TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA -+ -CCCFFFFFHHHHDEE,EFFGFGGDEEGHHGGFGCGFFCFFGFEFFFDFGCHFE8 -@HS21_09876:2:1105:10717:93499#75 -TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA -+ -CCCFFFFFHHHHDEB6DFFFDG;EEFFFAGHFGFGFFAFFGEGFFFFFGCH:9F -@HS21_09876:2:2107:17307:90872#75 -TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC -+ -BCCDFEFDHHFHDAE7FFFFFGGFHGGHHGFFGGGEFFFFGGEFFFFFDFHEEG -@HS21_09876:2:2108:10562:66996#75 -TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC -+ -CCCFFFFEHHFFDEE6FFDIGGGF>GFHHGFFGFGFFFFFGEGFFFFFDFFFCD -@HS21_09876:2:1204:3124:19338#75 -TAAGAGTCAGGGGTGCAGACCGGCGTGATGGAGGGCGCGCGGATGCCGTTCGGC -+ -CCCFFFFFHHHHDAE6FFGEIGGEHDGHHGGFGFDEFFFEGEEFFFFFDEEFFF -@HS21_09876:2:1104:8314:51088#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -CCCFFFFFHGDFFEE1GFGEFGGEDDGDH>GAGFGFFHFFGGECFFFFGFHBDC -@HS21_09876:2:1205:9430:9196#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -BBCDFFFFHHHHDEE7FFFGDGGEHEFHHFHFGFGDFFFFGGGFFFFFDFEFCC -@HS21_09876:2:1211:6841:16284#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -BCCFFFFFHHHHDDE1FEDEE=GEFGFHHGGEGFG>FFFCGCG@FF@FDGF@DE -@HS21_09876:2:2101:5488:100342#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -CCCFFFDDHHHHDEE3FFGCD=GFEGFHHEGEGFFDFGFEGDEFFFFFGFEFB8 -@HS21_09876:2:2109:9412:27195#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -BCCFFFFEHGBCC@<,D>GF:CGFDGGD=GG6ACDDF@FFGDECFFFF7EEDE. -@HS21_09876:2:2208:5757:63730#75 -TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT -+ -BCCDDEFFHFHHFEE6FIFEEGGFEFIF=GHGGHGFFH>FGEG9FFEFDFHFEB Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradis/test2.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test2.tagged.fastq.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradis/test.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradis/test.tagged.fastq 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 @@ -1,112 +0,0 @@ -@HS21_09876:1:1105:9650:48712#84 -TAAGATTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF -@HS21_09876:1:1106:8638:38957#84 -TGAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD -@HS21_09876:1:1105:9650:48712#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF -@HS21_09876:1:1106:8638:38957#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD -@HS21_09876:1:1204:19746:42237#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF -@HS21_09876:1:2210:2408:11148#83 -TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG -+ -BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE -@HS21_09876:1:1201:6607:66324#83 -TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD -@HS21_09876:1:2102:12312:75235#83 -TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT -+ -BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE -@HS21_09876:1:1106:16061:54950#83 -TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC -+ -BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD -@HS21_09876:1:2207:12005:97464#83 -TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG -+ -BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D -@HS21_09876:1:1208:12319:4648#83 -TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC -+ -B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF -@HS21_09876:2:1211:5990:82312#83 -TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC -+ -BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE -@HS21_09876:2:2103:19946:55809#83 -TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC -+ -BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF -@HS21_09876:1:1115:10349:43433#83 -TTTTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCNNACNCTNN -+ -8,(,*AHGFEDDCFG8CE=FF8BB7ED?FEEE522!!<2!:0!! -@HS21_09876:1:1211:4356:84410#83 -TTCTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCTGACTCTTA -+ ->E52EHFGFFGGFFFGHGHEEEGFGEGFGFGFGCGGFGFGFDHHHHFFFFFCCC -@HS21_09876:1:1101:19209:27276#83 -CGCACAGCCGTGTGGAAAAAACCGCTGTGGATAACCATCTCGGCCTGACTCTTA -+ -CEF4GHFDFFEEIFECHFGEFFGFEFGFGFFFGDHGHGFEFFHHHHFFFFFCCC Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradis/test.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradis/test.tagged.fastq.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/expected.1mm.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/expected.1mm.plot.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/expected.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/expected.plot.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/filelist.txt bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/filelist.txt --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/filelist.txt 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/filelist.txt 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,2 @@ +test.tagged.fastq +test2.tagged.fastq diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/filtered.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/filtered.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/filtered.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/filtered.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/mapped.sam bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/mapped.sam --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/mapped.sam 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/mapped.sam 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,25 @@ +@SQ SN:AE004091 LN:9840 +@PG ID:bwa PN:bwa VN:0.7.17-r1194-dirty CL:bwa mem -k 13 -t 4 smallref.fa test.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7058 60 44M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 MD:Z:38 AS:i:38 XS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 60 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 MD:Z:42 AS:i:42 XS:i:0 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 60 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:2 MD:Z:0G11T31 AS:i:38 XS:i:0 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3184 60 44M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:1 MD:Z:0G43 AS:i:43 XS:i:0 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3957 60 44M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:1 MD:Z:0T43 AS:i:43 XS:i:0 diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/notags.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/notags.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/notags.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/notags.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/smallref.fa bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/smallref.fa --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/smallref.fa 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/smallref.fa 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,165 @@ +>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome. +tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat +gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc +tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc +ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg +gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta +cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc +ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc +ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat +ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc +aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg +tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc +tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca +gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc +cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag +tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg +agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg +cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca +accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg +ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg +gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga +acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg +ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt +tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca +ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga +aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg +ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg +cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg +tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc +cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc +tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg +atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc +tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg +atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg +atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag +gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa +ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg +gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt +cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg +atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag +aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat +ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg +cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc +aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac +cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc +gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc +ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg +aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag +ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc +aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg +aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac +ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag +caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat +gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc +cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc +atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac +ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag +gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg +gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg +agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg +ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg +gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc +tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc +ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta +ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga +ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag +cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt +cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc +atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac +gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat +ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc +acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc +atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga +aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca +ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg +gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca +atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga +tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg +gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca +tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac +tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg +agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt +ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc +tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg +cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag +tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc +cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga +acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg +atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct +cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg +gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca +agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc +gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg +acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc +agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg +aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc +tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca +tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct +tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt +tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag +agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg +gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc +tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta +ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc +aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag +accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct +acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg +gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc +gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc +acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca +ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg +accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa +gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg +aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca +ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac +ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc +gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc +ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca +cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat +ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc +gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca +gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc +gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg +cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt +ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag +ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag +tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat +cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac +cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc +gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc +ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga +ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct +ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa +tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac +agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag +tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc +tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag +ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg +cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa +tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc +gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc +ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg +aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt +gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc +acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg +ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt +tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc +atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac +cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg +cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg +gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg +acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac +ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga +ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat +ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat +cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg +gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg +attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg +gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc +ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc +aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg +ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac +aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc +gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac +gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test2.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test2.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test2.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test2.tagged.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,452 @@ +@HS21_09876:1:1207:4978:63940#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHGHC7E4EEFGFFGGFFFCEG@EHGFFEGFEGFFEGEHFFGFGFE +@HS21_09876:1:1203:13201:16985#75 +TAAGAGTCAGCGGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGA ++ +BCCFFFFFGHHHCED9GEFDEFGFIFEGCEFEHGGFGGFFGFFGGEFGHGEGFF +@HS21_09876:1:1105:14817:70208#75 +TAAGAGTCAGGCCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGACGAAGCCC ++ +CCCFFFFFHHHHCEF8HHFGCFGGEFEFEGGEFFGFFGFFGFGFGEGGHGFEFE +@HS21_09876:1:1101:1155:30938#75 +TAAGAGTCAGGTTGCATAACTCGACGAAGCCCAGCAACTGCGTGTTTCTCCGGC ++ +B=?DDDEFHCFHBDD,AEFEGDGGCFFGE>DEAHEFFFCFGFFFDEGEFGFFFE +@HS21_09876:1:2204:6930:62477#75 +TAAGAGTCAGGGGCAAAAGGTTGTCGAGAACCGGTGTCGAGGCTGTTTCCTTCC ++ +BBCFFFFFHHHHCEF5GHFFCFDGEFBCHFFEFFGFFGFFGFFDGEEGFGFGFE +@HS21_09876:1:2211:14592:36752#75 +TAAGAGTCAGGGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTCCCCC ++ +CCCFFFFFHFHH9BF%GGFFEFDGFFF;EFFEHGGFEGFFGFFEGDEFHGFGFE +@HS21_09876:1:1101:1117:56616#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +=:=DADDDFFHHCDF8EEFGGFGEEFDGHEEEGGCFFFFFGFGFGCGGFGE@ED +@HS21_09876:1:1106:9993:12675#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +BBBFFFFFHHFHCBI2DEFGGFGEFFFGHGIEHHGFFGFFGFFJGEHFFGFDFE +@HS21_09876:1:2205:12308:83747#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +BCCFFFFFHHHHC@F7EEFGFFGFEFGGGFHEGEFFFGFFGFFECDEGHGFFFF +@HS21_09876:1:2211:5325:48675#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +1:B4A2AD2ACF57<'GE4EEFG9@FDDGGIEE?F:=8FEGFGDGACGFGEDA: +@HS21_09876:1:1202:13852:46659#75 +TAAGAGTCAGGGGCCAACGGCATCGCCAGCAACCTGGGGATTTCCCGTGAGCGC ++ +CCCFFFFFHHHHCEH8EEFGFFDG7FG;EFFEAHEFGGFFBFGEGEGGFGEGFF +@HS21_09876:1:1110:4160:49896#75 +TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG ++ +BCBFFFFDHHHHCDF8AEFGCFGHDFGCHGDEFFGFFGGFGFGFG8GGHGFFFE +@HS21_09876:1:2205:9754:20814#75 +TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG ++ +BBCFDEFEHHHHCEE4EIFGGFAFEFGGHFFEGEFFGGFEGFFFGEFEHGFEFF +@HS21_09876:1:1104:13063:60859#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHH>0@F,GEFE3CHEEFDC2FEEAG?FCEFED=F8CEEEH;;EDE +@HS21_09876:1:1107:8692:25384#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +@@CFFFFFHHHHA@E7EIFEEFGE-F@EHDCFF8G>GFFBGCCCHGF:AD +@HS21_09876:1:1109:11137:7630#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BCCFFFFFHHGHCBF8EEFDEFGEEFGG>GFEGGCFFGGFGFFEGGFFHGFEFF +@HS21_09876:1:1110:7663:40978#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@=DADDHDFH?7D9EGFFEFGFEFF;>FDED?FFEGGEGFGFACFFFGFFFE +@HS21_09876:1:1201:5332:2719#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BCCFFFFFHHHHADF4EHFEEFGFEFEGCG@EEFCFFGFFGFGFGEEGHGFFFD +@HS21_09876:1:1204:12364:36595#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBD2EGFFFFEDFEFFGFFGFGEGEGEHGFGFF +@HS21_09876:1:2102:4320:20528#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBBFFFDDFFHHCEF2EEFGCFGEEGED>G@EEGEFGGGEGFGEBCEGHGFEED +@HS21_09876:1:2102:17907:93005#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE5EEFFEFGEEFEGFEEEDFCFGGFFGFFGGGFGHGFEFF +@HS21_09876:1:2104:19430:56353#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCDFFFEHHHHCBH5FGFEEFGEDEFG>EHEEEEFFGGEGFFEGDGGFGFGFE +@HS21_09876:1:2106:8768:77924#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBE7EGFFEFG87CEDFEFEFHCFFGFFGFFEGEGEHGFEDF +@HS21_09876:1:2109:3560:75405#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@@DFDDFHHHHCBD,FGFEFIEGGFFGGGFGFFEGEFGFGFEFD +@HS21_09876:1:2201:7109:15683#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF5GHFECFGEFFEGEGEEEFFFEGFFGFFGGGEFHGFEFF +@HS21_09876:1:2204:5779:59154#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFEHHHHCEF7EEFFE@EHGFFFGGEGFFDCEEGHGEFFE +@HS21_09876:1:2210:14908:13619#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHFHHC7H,EEFGDEEAFGF=GA>GFG8GCGGHGFDFD +@HS21_09876:1:2210:1263:58662#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBBFFFFFHHHGBBH4HE?FE@GC7GFDFEDEAHCFFG;>GFGFG8EEHGF@DD +@HS21_09876:1:2211:14421:77160#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHFFF;EE-HEFFCFGCDFGDFFHEDFFFGGFEGFGEGEGGHGFGEF +@HS21_09876:1:1107:18833:61679#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +CCCFFFFFHHHH87E,G24E<9IE-FGFFG/1GFFFGEGE=;FGFC +@HS21_09876:1:1201:13166:59616#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHCDF5GEFFEFEFEFFDEGGEHGEFEEFFGFGFGDEGHGFGFD +@HS21_09876:1:1205:1312:68078#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +B@@FFFFFHHHHCDE,GEFCEFEFEFDGCGFEGGGFFEFEGFFEGECEHGFFFE +@HS21_09876:1:2101:9743:73722#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHCDF7EEFFEFGFEFBDFEHEEFGFFFFFGFGFGEEEFGFEFE +@HS21_09876:1:2112:4406:21609#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BBCDFFFFHHHD-<<+8=FHEGFGGFEGFE?GDGG=GDFBE +@HS21_09876:1:2207:5093:25809#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BBCDDEFDHHFFCBF,FEFECFGFFFF;HGGEFFEFEGFFGFGDGEGGHGFFBE +@HS21_09876:1:1105:3593:46102#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +CCCFFFFFHHHHCDE4EGFGECGFEFFEGFEEGFEFEGGEGFFJGFFGHGFGFF +@HS21_09876:1:1214:11162:39342#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +BCCDDFFFHHHHCB<&3GFEFFGGEFFDFGDEHGECGGGFGFFFGEEGFDFEFD +@HS21_09876:1:2103:18144:97839#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +CCCFFFFFHHGFCEE'EIFFGFDFDFECGGHEFGGFFCGFGFGDGEGEHGFEFD +@HS21_09876:1:1109:10864:56828#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +BCCDFFFFHHHFABE2EHFGCFEEEDFEAF?FEGAD==GE98EG=G@@ED +@HS21_09876:1:2108:6881:4925#75 +TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA ++ +CCCFFFEEHHHHCEE0EEFGFFGGEFDGHEFEEFGFGFGFGFGDGDEEHGDEFE +@HS21_09876:1:1111:18499:9859#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +BBCFFFFFHHHHCEF0GEFDEFEFIFFGGGFEHDGFFGGFGFFEGEGFHGFGFF +@HS21_09876:1:1210:19511:97335#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +CCCFFFFDHFFHCDH7HGFGGFGEIFFGHGHEFFGFFGFEGFFGGGGEHGFEFD +@HS21_09876:1:1103:13218:78186#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHHHHCDF7EEFDC9GEFFECEEFEHGGFGGFFGFFFGGFGFGFFFC +@HS21_09876:1:2107:11891:7630#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +@CCFFDDDHFFHCED0GIFDEFGEEFFDEFIEEFEFFEFEGFFBGEFGFGFEFD +@HS21_09876:1:2201:9833:67072#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHHHHCEE5GHFDEFGHDFEDFEGEEHGFGGFFGFGFGDGGFGFEFC +@HS21_09876:2:2101:20921:89053#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHHHD9E0FEFEGGGFHFFHHGGFGCFGFHFFGGGFFFFFGFEEEF +@HS21_09876:2:2205:9713:92092#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHHGED<6?EFEDG;:EEC;=GEAG@GFF;FGGCA9F>DFDFCE@E +@HS21_09876:2:2208:11577:65116#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +BBCFFDFFDFFA@AE3F3@D:GGFD:FHD>=FGFGD1GDAGF?FEGGDEFGFFGDG9FFFFFCG;AFFFFFGFEF9E +@HS21_09876:2:2103:7357:48165#75 +TAAGAGTCAGCCCATCCACCTGCTGGGCCTGGCGCGTTCATTCCGCAGTGCGCG ++ +CCCFFFFFHHHHDEE3GEDFGGGFEGGFHGFFGGGEFHFFGGGFFFFFDFHFEF +@HS21_09876:2:1102:4592:99056#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHDDE,FFGFFGGF-GIFCFGFGHDDFGFFGGEFFFFFEFFFED +@HS21_09876:2:1105:18701:63246#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHFDE3FFFEFGGDDFFFDEHEGHGFFFFF>GFFFFFFGFEFED +@HS21_09876:2:1107:9181:47786#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHFHHEDE1FFF4GGGEEFGFFGFHGHGFFHFFGEGFFFEFEFEFCE +@HS21_09876:2:2101:7072:68459#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHDEE3FFFFDGGF7EFHAFFGGFGEFHFFGGGFFFFFGFHFFD +@HS21_09876:2:2104:11024:92879#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHDDE7FFDG:GGDEEFF=GGFAHFFFFFGGEEFFFFFGFEFEF +@HS21_09876:2:2106:9334:51625#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@FBDADFHHFEA<1FFG::=GFH0=;1>=FA@D>FAF<>;A9FFFFG?=B9E +@HS21_09876:2:2107:14640:85151#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@BDDFFHHFHFEE,FIDFDGGDFFGF=GHGGHFFFHFHGEGFFF@FGEEEDD +@HS21_09876:2:2201:18727:56295#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B=BDFFFFHHD>EAE3GDFCD=GEEDGH1>C6GGD>FG3FGHEFFF0F7EEDDC +@HS21_09876:2:2203:20492:60041#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFEHFFFCEE'FFFFDGGEEGGFAFFFGHGDFHFFGHGFFFFFGEEEEF +@HS21_09876:2:1102:1602:23426#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBCFFFFFHHFHDAE6FFDEGGGDC:FDHEGHA@GGFGFFGEGFFFFFGEFBFE +@HS21_09876:2:1104:6936:48990#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +CCCFFFFFHHHHDEE,FFFEGGGDF:F;HFGFGFGEFGFFGGEGFFFFGFFFEF +@HS21_09876:2:2101:9813:71457#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCDFFFFHHHHEEE3FIDEGGGDEDFAHGGGGGGGFFFFGHEFFFFFEFHDEF +@HS21_09876:2:2201:13960:2115#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCFFFFFHHHHFEE4FFGEGGGDFAGDHGHGGGGFFGFFGEDFFFFFDFHDED +@HS21_09876:2:2202:14819:44089#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +CCCFFFFFHHHHD9E4GFFFIGGDF:GDHGGGGHGFFFFFGEEGFFFFEFEEEG +@HS21_09876:2:2203:10287:44498#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCFFFFFHHHHDEE6GIFEGGGDDDGHHGGFGFGFFFFEGFFGFFFFGFEEEF +@HS21_09876:2:2206:9622:55348#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBCFFFFFHHHHDDE,FFFEGGGDFAGHHGGFGHFDFFFFGGDFFFFFDEHEEE +@HS21_09876:2:1101:1182:4708#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BBBFFFFFHHGHF=E6EFFEEGGGFDGGEGFAGFGFFCFFGHEFFFEFFGFEED +@HS21_09876:2:2207:16105:64688#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHFEE1FFDDDGBFEGCFAFFEGHDEFCFEGDF9F;@EFGG:EEFH=FCEG3FF<;FFGHFFFFDFGECEDF +@HS21_09876:2:1212:2848:49763#75 +TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG ++ +BCCDDEFFHGGHFDE,DDEDHG;E;FG;HFGEGFGDFF3FGEGFFFFF7FFF9D +@HS21_09876:2:2101:18079:59533#75 +TAAGAGTCAGCCCGTGAAACGCCTGAAAAAGACACTGCACCTTTCAAGCTTGTC ++ +@@@DDDDDHHA+9AB1F>G01AG:CD1H=>CEA3F3FA>FAFEGEGFFFEFGFEEEE +@HS21_09876:2:1111:18613:97316#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BBCBDFFFHHHHDAE,EFFFGGGEEEGADEHFGCGDFGFFGGGFFFFFDGEFCE +@HS21_09876:2:2112:7311:2729#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BCCDFEFEHFFH7EE)GEGFFGGGCEI;HGGFGFGFFHFEGEG6FFDFECC76D +@HS21_09876:2:2209:5184:70364#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +CCCFFFFFHFFHDEE7FFFGFGGGDGGHHGGFGFGDFCFFGEEGFFFFEFFFEF +@HS21_09876:2:2206:10363:37150#75 +TAAGAGTCAGGGGGCTTCACCGTAGCCGGCACGGGCGCCCGGCAGATGGTCGGC ++ +BBBFFFFFHHHHDDE1FF@HIGGE?GGFHFEFGHGEFFFFGFGFFFFFGEEFBE +@HS21_09876:2:1211:8018:71514#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +BBCDDEDFHHGHDAE,FEDE:2;ECF=H=>GF5@G>FGFH3CGFFF@FDEEF9E +@HS21_09876:2:2207:12305:87719#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +@@CADAADFFFFFEE6FEGFGGGFEFFHHGGFGHGFFHFEGHEFFFEFGFEDEB +@HS21_09876:2:1109:4620:60950#75 +TAAGAGTCAGAAAGCAGATCCTCGGGGCCAATCCGCCTCCCGGTGCGCGCGACG ++ +CCCFFFFFHHHHDEE4FFFEGGGHFGGFHFCFGFGEFHFFGGEGFFFFDFEFCE +@HS21_09876:2:1108:17674:57476#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +CCCFFFFFHHHHFEE4FFDGIGGGFGGFHGGFGGGFFFFFGFFFFFFFDFHFEC +@HS21_09876:2:1208:4027:38154#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +BCCFFFFFHHHHFEE6GFFEIGGGCGFFHGGFGGGEFGFFGFGFFFFFDFHFFE +@HS21_09876:2:2104:21108:77778#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +CCCFFFFFHHHHDEE,EFFGFGGDEEGHHGGFGCGFFCFFGFEFFFDFGCHFE8 +@HS21_09876:2:1105:10717:93499#75 +TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA ++ +CCCFFFFFHHHHDEB6DFFFDG;EEFFFAGHFGFGFFAFFGEGFFFFFGCH:9F +@HS21_09876:2:2107:17307:90872#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +BCCDFEFDHHFHDAE7FFFFFGGFHGGHHGFFGGGEFFFFGGEFFFFFDFHEEG +@HS21_09876:2:2108:10562:66996#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +CCCFFFFEHHFFDEE6FFDIGGGF>GFHHGFFGFGFFFFFGEGFFFFFDFFFCD +@HS21_09876:2:1204:3124:19338#75 +TAAGAGTCAGGGGTGCAGACCGGCGTGATGGAGGGCGCGCGGATGCCGTTCGGC ++ +CCCFFFFFHHHHDAE6FFGEIGGEHDGHHGGFGFDEFFFEGEEFFFFFDEEFFF +@HS21_09876:2:1104:8314:51088#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHGDFFEE1GFGEFGGEDDGDH>GAGFGFFHFFGGECFFFFGFHBDC +@HS21_09876:2:1205:9430:9196#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BBCDFFFFHHHHDEE7FFFGDGGEHEFHHFHFGFGDFFFFGGGFFFFFDFEFCC +@HS21_09876:2:1211:6841:16284#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCFFFFFHHHHDDE1FEDEE=GEFGFHHGGEGFG>FFFCGCG@FF@FDGF@DE +@HS21_09876:2:2101:5488:100342#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFDDHHHHDEE3FFGCD=GFEGFHHEGEGFFDFGFEGDEFFFFFGFEFB8 +@HS21_09876:2:2109:9412:27195#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCFFFFEHGBCC@<,D>GF:CGFDGGD=GG6ACDDF@FFGDECFFFF7EEDE. +@HS21_09876:2:2208:5757:63730#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCDDEFFHFHHFEE6FIFEEGGFEFIF=GHGGHGFFH>FGEG9FFEFDFHFEB Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test2.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test2.tagged.fastq.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test.tagged.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,112 @@ +@HS21_09876:1:1105:9650:48712#84 +TAAGATTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#84 +TGAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1105:9650:48712#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF +@HS21_09876:1:1115:10349:43433#83 +TTTTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCNNACNCTNN ++ +8,(,*AHGFEDDCFG8CE=FF8BB7ED?FEEE522!!<2!:0!! +@HS21_09876:1:1211:4356:84410#83 +TTCTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCTGACTCTTA ++ +>E52EHFGFFGGFFFGHGHEEEGFGEGFGFGFGCGGFGFGFDHHHHFFFFFCCC +@HS21_09876:1:1101:19209:27276#83 +CGCACAGCCGTGTGGAAAAAACCGCTGTGGATAACCATCTCGGCCTGACTCTTA ++ +CEF4GHFDFFEEIFECHFGEFFGFEFGFGFFFGDHGHGFEFFHHHHFFFFFCCC Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisBWA/test.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisBWA/test.tagged.fastq.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/expected.1mm.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/expected.1mm.plot.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/expected.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/expected.plot.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/filelist.txt bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/filelist.txt --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/filelist.txt 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/filelist.txt 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,2 @@ +test.tagged.fastq +test2.tagged.fastq diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/filtered.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/filtered.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/filtered.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/filtered.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/mapped.sam bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/mapped.sam --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/mapped.sam 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/mapped.sam 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,26 @@ +@HD VN:1.3 SO:unknown +@SQ SN:AE004091 LN:9840 +@PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/RunTradis/notags.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43 diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/notags.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/notags.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/notags.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/notags.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/smallref.fa bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/smallref.fa --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/smallref.fa 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/smallref.fa 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,165 @@ +>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome. +tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat +gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc +tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc +ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg +gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta +cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc +ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc +ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat +ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc +aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg +tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc +tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca +gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc +cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag +tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg +agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg +cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca +accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg +ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg +gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga +acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg +ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt +tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca +ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga +aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg +ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg +cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg +tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc +cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc +tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg +atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc +tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg +atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg +atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag +gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa +ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg +gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt +cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg +atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag +aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat +ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg +cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc +aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac +cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc +gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc +ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg +aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag +ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc +aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg +aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac +ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag +caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat +gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc +cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc +atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac +ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag +gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg +gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg +agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg +ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg +gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc +tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc +ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta +ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga +ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag +cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt +cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc +atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac +gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat +ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc +acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc +atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga +aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca +ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg +gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca +atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga +tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg +gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca +tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac +tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg +agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt +ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc +tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg +cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag +tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc +cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga +acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg +atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct +cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg +gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca +agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc +gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg +acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc +agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg +aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc +tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca +tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct +tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt +tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag +agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg +gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc +tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta +ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc +aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag +accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct +acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg +gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc +gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc +acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca +ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg +accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa +gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg +aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca +ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac +ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc +gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc +ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca +cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat +ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc +gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca +gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc +gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg +cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt +ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag +ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag +tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat +cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac +cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc +gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc +ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga +ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct +ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa +tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac +agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag +tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc +tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag +ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg +cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa +tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc +gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc +ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg +aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt +gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc +acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg +ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt +tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc +atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac +cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg +cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg +gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg +acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac +ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga +ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat +ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat +cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg +gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg +attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg +gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc +ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc +aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg +ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac +aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc +gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac +gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test2.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test2.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test2.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test2.tagged.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,452 @@ +@HS21_09876:1:1207:4978:63940#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHGHC7E4EEFGFFGGFFFCEG@EHGFFEGFEGFFEGEHFFGFGFE +@HS21_09876:1:1203:13201:16985#75 +TAAGAGTCAGCGGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGA ++ +BCCFFFFFGHHHCED9GEFDEFGFIFEGCEFEHGGFGGFFGFFGGEFGHGEGFF +@HS21_09876:1:1105:14817:70208#75 +TAAGAGTCAGGCCTCTTGGGACGGCGCTTTTCTGTGCATAACTCGACGAAGCCC ++ +CCCFFFFFHHHHCEF8HHFGCFGGEFEFEGGEFFGFFGFFGFGFGEGGHGFEFE +@HS21_09876:1:1101:1155:30938#75 +TAAGAGTCAGGTTGCATAACTCGACGAAGCCCAGCAACTGCGTGTTTCTCCGGC ++ +B=?DDDEFHCFHBDD,AEFEGDGGCFFGE>DEAHEFFFCFGFFFDEGEFGFFFE +@HS21_09876:1:2204:6930:62477#75 +TAAGAGTCAGGGGCAAAAGGTTGTCGAGAACCGGTGTCGAGGCTGTTTCCTTCC ++ +BBCFFFFFHHHHCEF5GHFFCFDGEFBCHFFEFFGFFGFFGFFDGEEGFGFGFE +@HS21_09876:1:2211:14592:36752#75 +TAAGAGTCAGGGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTCCCCC ++ +CCCFFFFFHFHH9BF%GGFFEFDGFFF;EFFEHGGFEGFFGFFEGDEFHGFGFE +@HS21_09876:1:1101:1117:56616#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +=:=DADDDFFHHCDF8EEFGGFGEEFDGHEEEGGCFFFFFGFGFGCGGFGE@ED +@HS21_09876:1:1106:9993:12675#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +BBBFFFFFHHFHCBI2DEFGGFGEFFFGHGIEHHGFFGFFGFFJGEHFFGFDFE +@HS21_09876:1:2205:12308:83747#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +BCCFFFFFHHHHC@F7EEFGFFGFEFGGGFHEGEFFFGFFGFFECDEGHGFFFF +@HS21_09876:1:2211:5325:48675#75 +TAAGAGTCAGGGGCCTGCACCGTATTCGGCCAGGTGATGTTGGCCAACGGCATC ++ +1:B4A2AD2ACF57<'GE4EEFG9@FDDGGIEE?F:=8FEGFGDGACGFGEDA: +@HS21_09876:1:1202:13852:46659#75 +TAAGAGTCAGGGGCCAACGGCATCGCCAGCAACCTGGGGATTTCCCGTGAGCGC ++ +CCCFFFFFHHHHCEH8EEFGFFDG7FG;EFFEAHEFGGFFBFGEGEGGFGEGFF +@HS21_09876:1:1110:4160:49896#75 +TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG ++ +BCBFFFFDHHHHCDF8AEFGCFGHDFGCHGDEFFGFFGGFGFGFG8GGHGFFFE +@HS21_09876:1:2205:9754:20814#75 +TAAGAGTCAGAAACTCTCCCACTGCAACTGATCAACCCGGACAGCTTTCGGTTG ++ +BBCFDEFEHHHHCEE4EIFGGFAFEFGGHFFEGEFFGGFEGFFFGEFEHGFEFF +@HS21_09876:1:1104:13063:60859#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHH>0@F,GEFE3CHEEFDC2FEEAG?FCEFED=F8CEEEH;;EDE +@HS21_09876:1:1107:8692:25384#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +@@CFFFFFHHHHA@E7EIFEEFGE-F@EHDCFF8G>GFFBGCCCHGF:AD +@HS21_09876:1:1109:11137:7630#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BCCFFFFFHHGHCBF8EEFDEFGEEFGG>GFEGGCFFGGFGFFEGGFFHGFEFF +@HS21_09876:1:1110:7663:40978#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@=DADDHDFH?7D9EGFFEFGFEFF;>FDED?FFEGGEGFGFACFFFGFFFE +@HS21_09876:1:1201:5332:2719#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BCCFFFFFHHHHADF4EHFEEFGFEFEGCG@EEFCFFGFFGFGFGEEGHGFFFD +@HS21_09876:1:1204:12364:36595#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBD2EGFFFFEDFEFFGFFGFGEGEGEHGFGFF +@HS21_09876:1:2102:4320:20528#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBBFFFDDFFHHCEF2EEFGCFGEEGED>G@EEGEFGGGEGFGEBCEGHGFEED +@HS21_09876:1:2102:17907:93005#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE5EEFFEFGEEFEGFEEEDFCFGGFFGFFGGGFGHGFEFF +@HS21_09876:1:2104:19430:56353#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCDFFFEHHHHCBH5FGFEEFGEDEFG>EHEEEEFFGGEGFFEGDGGFGFGFE +@HS21_09876:1:2106:8768:77924#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBE7EGFFEFG87CEDFEFEFHCFFGFFGFFEGEGEHGFEDF +@HS21_09876:1:2109:3560:75405#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@@DFDDFHHHHCBD,FGFEFIEGGFFGGGFGFFEGEFGFGFEFD +@HS21_09876:1:2201:7109:15683#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF5GHFECFGEFFEGEGEEEFFFEGFFGFFGGGEFHGFEFF +@HS21_09876:1:2204:5779:59154#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFEHHHHCEF7EEFFE@EHGFFFGGEGFFDCEEGHGEFFE +@HS21_09876:1:2210:14908:13619#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHFHHC7H,EEFGDEEAFGF=GA>GFG8GCGGHGFDFD +@HS21_09876:1:2210:1263:58662#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBBFFFFFHHHGBBH4HE?FE@GC7GFDFEDEAHCFFG;>GFGFG8EEHGF@DD +@HS21_09876:1:2211:14421:77160#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHFFF;EE-HEFFCFGCDFGDFFHEDFFFGGFEGFGEGEGGHGFGEF +@HS21_09876:1:1107:18833:61679#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +CCCFFFFFHHHH87E,G24E<9IE-FGFFG/1GFFFGEGE=;FGFC +@HS21_09876:1:1201:13166:59616#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHCDF5GEFFEFEFEFFDEGGEHGEFEEFFGFGFGDEGHGFGFD +@HS21_09876:1:1205:1312:68078#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +B@@FFFFFHHHHCDE,GEFCEFEFEFDGCGFEGGGFFEFEGFFEGECEHGFFFE +@HS21_09876:1:2101:9743:73722#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHCDF7EEFFEFGFEFBDFEHEEFGFFFFFGFGFGEEEFGFEFE +@HS21_09876:1:2112:4406:21609#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BBCDFFFFHHHD-<<+8=FHEGFGGFEGFE?GDGG=GDFBE +@HS21_09876:1:2207:5093:25809#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BBCDDEFDHHFFCBF,FEFECFGFFFF;HGGEFFEFEGFFGFGDGEGGHGFFBE +@HS21_09876:1:1105:3593:46102#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +CCCFFFFFHHHHCDE4EGFGECGFEFFEGFEEGFEFEGGEGFFJGFFGHGFGFF +@HS21_09876:1:1214:11162:39342#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +BCCDDFFFHHHHCB<&3GFEFFGGEFFDFGDEHGECGGGFGFFFGEEGFDFEFD +@HS21_09876:1:2103:18144:97839#75 +TAAGAGTCAGGGGCTCAAGGCGTTGCGACAGCCGGATGGAACGCCTTTCCTCGC ++ +CCCFFFFFHHGFCEE'EIFFGFDFDFECGGHEFGGFFCGFGFGDGEGEHGFEFD +@HS21_09876:1:1109:10864:56828#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +BCCDFFFFHHHFABE2EHFGCFEEEDFEAF?FEGAD==GE98EG=G@@ED +@HS21_09876:1:2108:6881:4925#75 +TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA ++ +CCCFFFEEHHHHCEE0EEFGFFGGEFDGHEFEEFGFGFGFGFGDGDEEHGDEFE +@HS21_09876:1:1111:18499:9859#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +BBCFFFFFHHHHCEF0GEFDEFEFIFFGGGFEHDGFFGGFGFFEGEGFHGFGFF +@HS21_09876:1:1210:19511:97335#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +CCCFFFFDHFFHCDH7HGFGGFGEIFFGHGHEFFGFFGFEGFFGGGGEHGFEFD +@HS21_09876:1:1103:13218:78186#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHHHHCDF7EEFDC9GEFFECEEFEHGGFGGFFGFFFGGFGFGFFFC +@HS21_09876:1:2107:11891:7630#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +@CCFFDDDHFFHCED0GIFDEFGEEFFDEFIEEFEFFEFEGFFBGEFGFGFEFD +@HS21_09876:1:2201:9833:67072#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHHHHCEE5GHFDEFGHDFEDFEGEEHGFGGFFGFGFGDGGFGFEFC +@HS21_09876:2:2101:20921:89053#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHHHD9E0FEFEGGGFHFFHHGGFGCFGFHFFGGGFFFFFGFEEEF +@HS21_09876:2:2205:9713:92092#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +CCCFFFFFHHHGED<6?EFEDG;:EEC;=GEAG@GFF;FGGCA9F>DFDFCE@E +@HS21_09876:2:2208:11577:65116#75 +TAAGAGTCAGGGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTGC ++ +BBCFFDFFDFFA@AE3F3@D:GGFD:FHD>=FGFGD1GDAGF?FEGGDEFGFFGDG9FFFFFCG;AFFFFFGFEF9E +@HS21_09876:2:2103:7357:48165#75 +TAAGAGTCAGCCCATCCACCTGCTGGGCCTGGCGCGTTCATTCCGCAGTGCGCG ++ +CCCFFFFFHHHHDEE3GEDFGGGFEGGFHGFFGGGEFHFFGGGFFFFFDFHFEF +@HS21_09876:2:1102:4592:99056#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHDDE,FFGFFGGF-GIFCFGFGHDDFGFFGGEFFFFFEFFFED +@HS21_09876:2:1105:18701:63246#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHFDE3FFFEFGGDDFFFDEHEGHGFFFFF>GFFFFFFGFEFED +@HS21_09876:2:1107:9181:47786#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHFHHEDE1FFF4GGGEEFGFFGFHGHGFFHFFGEGFFFEFEFEFCE +@HS21_09876:2:2101:7072:68459#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHDEE3FFFFDGGF7EFHAFFGGFGEFHFFGGGFFFFFGFHFFD +@HS21_09876:2:2104:11024:92879#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHDDE7FFDG:GGDEEFF=GGFAHFFFFFGGEEFFFFFGFEFEF +@HS21_09876:2:2106:9334:51625#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@FBDADFHHFEA<1FFG::=GFH0=;1>=FA@D>FAF<>;A9FFFFG?=B9E +@HS21_09876:2:2107:14640:85151#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BB@BDDFFHHFHFEE,FIDFDGGDFFGF=GHGGHFFFHFHGEGFFF@FGEEEDD +@HS21_09876:2:2201:18727:56295#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B=BDFFFFHHD>EAE3GDFCD=GEEDGH1>C6GGD>FG3FGHEFFF0F7EEDDC +@HS21_09876:2:2203:20492:60041#75 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFEHFFFCEE'FFFFDGGEEGGFAFFFGHGDFHFFGHGFFFFFGEEEEF +@HS21_09876:2:1102:1602:23426#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBCFFFFFHHFHDAE6FFDEGGGDC:FDHEGHA@GGFGFFGEGFFFFFGEFBFE +@HS21_09876:2:1104:6936:48990#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +CCCFFFFFHHHHDEE,FFFEGGGDF:F;HFGFGFGEFGFFGGEGFFFFGFFFEF +@HS21_09876:2:2101:9813:71457#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCDFFFFHHHHEEE3FIDEGGGDEDFAHGGGGGGGFFFFGHEFFFFFEFHDEF +@HS21_09876:2:2201:13960:2115#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCFFFFFHHHHFEE4FFGEGGGDFAGDHGHGGGGFFGFFGEDFFFFFDFHDED +@HS21_09876:2:2202:14819:44089#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +CCCFFFFFHHHHD9E4GFFFIGGDF:GDHGGGGHGFFFFFGEEGFFFFEFEEEG +@HS21_09876:2:2203:10287:44498#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BCCFFFFFHHHHDEE6GIFEGGGDDDGHHGGFGFGFFFFEGFFGFFFFGFEEEF +@HS21_09876:2:2206:9622:55348#75 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBCFFFFFHHHHDDE,FFFEGGGDFAGHHGGFGHFDFFFFGGDFFFFFDEHEEE +@HS21_09876:2:1101:1182:4708#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BBBFFFFFHHGHF=E6EFFEEGGGFDGGEGFAGFGFFCFFGHEFFFEFFGFEED +@HS21_09876:2:2207:16105:64688#75 +TAAGAGTCAGGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTCGGCGC ++ +BCCFFFFFHHHHFEE1FFDDDGBFEGCFAFFEGHDEFCFEGDF9F;@EFGG:EEFH=FCEG3FF<;FFGHFFFFDFGECEDF +@HS21_09876:2:1212:2848:49763#75 +TAAGAGTCAGCCCCCTACGCTGGACAATCTGTACTAGATTCAATAATGGCAATG ++ +BCCDDEFFHGGHFDE,DDEDHG;E;FG;HFGEGFGDFF3FGEGFFFFF7FFF9D +@HS21_09876:2:2101:18079:59533#75 +TAAGAGTCAGCCCGTGAAACGCCTGAAAAAGACACTGCACCTTTCAAGCTTGTC ++ +@@@DDDDDHHA+9AB1F>G01AG:CD1H=>CEA3F3FA>FAFEGEGFFFEFGFEEEE +@HS21_09876:2:1111:18613:97316#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BBCBDFFFHHHHDAE,EFFFGGGEEEGADEHFGCGDFGFFGGGFFFFFDGEFCE +@HS21_09876:2:2112:7311:2729#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +BCCDFEFEHFFH7EE)GEGFFGGGCEI;HGGFGFGFFHFEGEG6FFDFECC76D +@HS21_09876:2:2209:5184:70364#75 +TAAGAGTCAGCCCCCTGCCCTGGCTCAAGGCGTTGCGACAGCCGGATGGAACGC ++ +CCCFFFFFHFFHDEE7FFFGFGGGDGGHHGGFGFGDFCFFGEEGFFFFEFFFEF +@HS21_09876:2:2206:10363:37150#75 +TAAGAGTCAGGGGGCTTCACCGTAGCCGGCACGGGCGCCCGGCAGATGGTCGGC ++ +BBBFFFFFHHHHDDE1FF@HIGGE?GGFHFEFGHGEFFFFGFGFFFFFGEEFBE +@HS21_09876:2:1211:8018:71514#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +BBCDDEDFHHGHDAE,FEDE:2;ECF=H=>GF5@G>FGFH3CGFFF@FDEEF9E +@HS21_09876:2:2207:12305:87719#75 +TAAGAGTCAGCCCGCTGACCAGCGATGACGCCGCCTTCGACGCCTTCGCCAAGC ++ +@@CADAADFFFFFEE6FEGFGGGFEFFHHGGFGHGFFHFEGHEFFFEFGFEDEB +@HS21_09876:2:1109:4620:60950#75 +TAAGAGTCAGAAAGCAGATCCTCGGGGCCAATCCGCCTCCCGGTGCGCGCGACG ++ +CCCFFFFFHHHHDEE4FFFEGGGHFGGFHFCFGFGEFHFFGGEGFFFFDFEFCE +@HS21_09876:2:1108:17674:57476#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +CCCFFFFFHHHHFEE4FFDGIGGGFGGFHGGFGGGFFFFFGFFFFFFFDFHFEC +@HS21_09876:2:1208:4027:38154#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +BCCFFFFFHHHHFEE6GFFEIGGGCGFFHGGFGGGEFGFFGFGFFFFFDFHFFE +@HS21_09876:2:2104:21108:77778#75 +TAAGAGTCAGCCCTTCCACCCGCAGAAGAGCAAGTTCCACCTGCTGGGCATGGA ++ +CCCFFFFFHHHHDEE,EFFGFGGDEEGHHGGFGCGFFCFFGFEFFFDFGCHFE8 +@HS21_09876:2:1105:10717:93499#75 +TAAGAGTCAGGGGGACACTCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCA ++ +CCCFFFFFHHHHDEB6DFFFDG;EEFFFAGHFGFGFFAFFGEGFFFFFGCH:9F +@HS21_09876:2:2107:17307:90872#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +BCCDFEFDHHFHDAE7FFFFFGGFHGGHHGFFGGGEFFFFGGEFFFFFDFHEEG +@HS21_09876:2:2108:10562:66996#75 +TAAGAGTCAGCCCGCTGAGGGACGTCGGCAGCGACAGCCGCCAGCACGCCATCC ++ +CCCFFFFEHHFFDEE6FFDIGGGF>GFHHGFFGFGFFFFFGEGFFFFFDFFFCD +@HS21_09876:2:1204:3124:19338#75 +TAAGAGTCAGGGGTGCAGACCGGCGTGATGGAGGGCGCGCGGATGCCGTTCGGC ++ +CCCFFFFFHHHHDAE6FFGEIGGEHDGHHGGFGFDEFFFEGEEFFFFFDEEFFF +@HS21_09876:2:1104:8314:51088#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFFFHGDFFEE1GFGEFGGEDDGDH>GAGFGFFHFFGGECFFFFGFHBDC +@HS21_09876:2:1205:9430:9196#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BBCDFFFFHHHHDEE7FFFGDGGEHEFHHFHFGFGDFFFFGGGFFFFFDFEFCC +@HS21_09876:2:1211:6841:16284#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCFFFFFHHHHDDE1FEDEE=GEFGFHHGGEGFG>FFFCGCG@FF@FDGF@DE +@HS21_09876:2:2101:5488:100342#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +CCCFFFDDHHHHDEE3FFGCD=GFEGFHHEGEGFFDFGFEGDEFFFFFGFEFB8 +@HS21_09876:2:2109:9412:27195#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCFFFFEHGBCC@<,D>GF:CGFDGGD=GG6ACDDF@FFGDECFFFF7EEDE. +@HS21_09876:2:2208:5757:63730#75 +TAAGAGTCAGCCCGTAGCGGTGGCCGGTTCGATCCTGCAGCACTTCGTGCCGAT ++ +BCCDDEFFHFHHFEE6FIFEEGGFEFIF=GHGGHGFFH>FGEG9FFEFDFHFEB Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test2.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test2.tagged.fastq.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test.tagged.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test.tagged.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test.tagged.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test.tagged.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,112 @@ +@HS21_09876:1:1105:9650:48712#84 +TAAGATTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#84 +TGAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1105:9650:48712#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +B@CFFFFFHHHHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +CCCFFFFFHHHHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +TAAGAGTCAGGGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +BBCFFFFFHHHHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFBDEHHHHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +TAAGAGTCAGCCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +BCCDFFFFHHHHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +TAAGAGTCAGGGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +BBBDFFFFHHFHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +TAAGAGTCAGGCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +BCCDFFFFHHHGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +TAAGAGTCAGCAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +B=BDFFFDH>AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TAAGAGTCAGTTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +BCCFFFFFHHHGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +TAAGAGTCAGGGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +BBCFDEFFHHHHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF +@HS21_09876:1:1115:10349:43433#83 +TTTTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCNNACNCTNN ++ +8,(,*AHGFEDDCFG8CE=FF8BB7ED?FEEE522!!<2!:0!! +@HS21_09876:1:1211:4356:84410#83 +TTCTCGACAACCTTTTGCCTGCCGGAGAAACACGCAGTTGCTACCTGACTCTTA ++ +>E52EHFGFFGGFFFGHGHEEEGFGEGFGFGFGCGGFGFGFDHHHHFFFFFCCC +@HS21_09876:1:1101:19209:27276#83 +CGCACAGCCGTGTGGAAAAAACCGCTGTGGATAACCATCTCGGCCTGACTCTTA ++ +CEF4GHFDFFEEIFECHFGEFFGFEFGFGFFFGDHGHGFEFFHHHHFFFFFCCC Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisSmalt/test.tagged.fastq.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisSmalt/test.tagged.fastq.gz differ Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/expected.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/expected.plot.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/filelist.txt bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/filelist.txt --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/filelist.txt 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/filelist.txt 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1 @@ +notags.fastq diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/mapped.sam bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/mapped.sam --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/mapped.sam 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/mapped.sam 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,25 @@ +@SQ SN:AE004091 LN:9840 +@PG ID:bwa PN:bwa VN:0.7.17-r1194-dirty CL:bwa mem -k 13 -t 4 smallref.fa test.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6697 60 44M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7025 60 44M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:1 MD:Z:0A43 AS:i:43 XS:i:0 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7058 60 44M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 MD:Z:38 AS:i:38 XS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 60 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 MD:Z:42 AS:i:42 XS:i:0 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 60 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:2 MD:Z:0G11T31 AS:i:38 XS:i:0 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3184 60 44M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:1 MD:Z:0G43 AS:i:43 XS:i:0 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3957 60 44M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:1 MD:Z:0T43 AS:i:43 XS:i:0 diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/notags.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/notags.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/notags.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/notags.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/smallref.fa bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/smallref.fa --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessBWA/smallref.fa 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessBWA/smallref.fa 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,165 @@ +>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome. +tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat +gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc +tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc +ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg +gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta +cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc +ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc +ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat +ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc +aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg +tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc +tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca +gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc +cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag +tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg +agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg +cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca +accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg +ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg +gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga +acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg +ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt +tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca +ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga +aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg +ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg +cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg +tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc +cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc +tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg +atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc +tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg +atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg +atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag +gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa +ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg +gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt +cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg +atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag +aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat +ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg +cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc +aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac +cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc +gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc +ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg +aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag +ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc +aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg +aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac +ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag +caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat +gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc +cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc +atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac +ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag +gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg +gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg +agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg +ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg +gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc +tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc +ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta +ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga +ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag +cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt +cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc +atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac +gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat +ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc +acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc +atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga +aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca +ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg +gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca +atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga +tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg +gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca +tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac +tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg +agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt +ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc +tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg +cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag +tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc +cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga +acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg +atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct +cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg +gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca +agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc +gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg +acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc +agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg +aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc +tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca +tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct +tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt +tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag +agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg +gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc +tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta +ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc +aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag +accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct +acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg +gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc +gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc +acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca +ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg +accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa +gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg +aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca +ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac +ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc +gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc +ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca +cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat +ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc +gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca +gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc +gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg +cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt +ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag +ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag +tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat +cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac +cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc +gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc +ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga +ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct +ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa +tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac +agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag +tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc +tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag +ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg +cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa +tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc +gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc +ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg +aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt +gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc +acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg +ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt +tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc +atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac +cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg +cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg +gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg +acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac +ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga +ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat +ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat +cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg +gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg +attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg +gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc +ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc +aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg +ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac +aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc +gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac +gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg Binary files /tmp/tmp2hd30W/lKSAs3gzEr/bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/expected.plot.gz and /tmp/tmp2hd30W/qxVFNe1xNn/bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/expected.plot.gz differ diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/mapped.sam bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/mapped.sam --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/mapped.sam 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/mapped.sam 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,26 @@ +@HD VN:1.3 SO:unknown +@SQ SN:AE004091 LN:9840 +@PG ID:smalt PN:smalt VN:0.7.4 CL:smalt map -x -r -1 -y 0.96 ref.index /Users/cc21/Development/repos/Bio-Tradis/t/data/RunTradis/notags.fastq +HS21_09876:1:1105:9650:48712#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF NM:i:0 AS:i:43 +HS21_09876:1:1106:8638:38957#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:1204:19746:42237#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF NM:i:0 AS:i:43 +HS21_09876:1:2210:2408:11148#83 0 AE004091 6698 54 1S43M * 0 0 GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE NM:i:0 AS:i:43 +HS21_09876:1:1201:6607:66324#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD NM:i:0 AS:i:43 +HS21_09876:1:2102:12312:75235#83 0 AE004091 7026 54 1S43M * 0 0 CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE NM:i:0 AS:i:43 +HS21_09876:1:1106:16061:54950#83 0 AE004091 7059 54 1S43M * 0 0 GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD NM:i:0 AS:i:0 +HS21_09876:1:2207:12005:97464#83 0 AE004091 9265 54 2S42M * 0 0 GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D NM:i:0 AS:i:42 +HS21_09876:1:1208:12319:4648#83 0 AE004091 9274 54 2S42M * 0 0 CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF NM:i:1 AS:i:40 +HS21_09876:2:1211:5990:82312#83 0 AE004091 3185 54 1S43M * 0 0 TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE NM:i:0 AS:i:43 +HS21_09876:2:2103:19946:55809#83 0 AE004091 3958 54 1S43M * 0 0 GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF NM:i:0 AS:i:43 diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/notags.fastq bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/notags.fastq --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/notags.fastq 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/notags.fastq 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,92 @@ +@HS21_09876:1:1105:9650:48712#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEE8EEFGFFGFIFGGFGEEHFFFGGGFGFGEGEEEFGFGFF +@HS21_09876:1:1106:8638:38957#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCEF7FHFFFFGFEGEFFEHEGEGFGGGEGFGFGGFEHGFEFD +@HS21_09876:1:1204:19746:42237#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF2GGFFEFGEEFFFEEHEEHFFFFGFGFFFGGGGHGFEFF +@HS21_09876:1:2210:2408:11148#83 +GGGTCGGCAGACCGACCCTCATGGAAACCCCGGCCTGGCGCCGG ++ +HHCBF,GGFFGEEEGFFGGFFGFFBG8FGFGFEEE +@HS21_09876:1:1201:6607:66324#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDF8EHFEGFAGIFEDEGFEFFGFEGFEGFGFGEGGHGFEFD +@HS21_09876:1:2102:12312:75235#83 +CCCACCGACGGCTCCGGATGGCTGACCCGCTGCTGGATGGGGCT ++ +HHCDH8EHFFGFAGDFIEEEGEFFGFFGFFGFFEGEFFFGFEFE +@HS21_09876:1:1106:16061:54950#83 +GGGATGGGGCTGATCTCGGCCATGGTCTCGCTGACCCAGGCTTC ++ +FHCBD4GHFFGFEEC8BI2AGDGFFGFEBFGDGEGEH;EFDD +@HS21_09876:1:2207:12005:97464#83 +GCCCCAAGGACACCTGGGGACCGGCGCGGCTGGACGCGGTATCG ++ +HGBBH0EG?DEDF?FFGFE1FE89EEGD;;@?D +@HS21_09876:1:1208:12319:4648#83 +CAACCTGGGGACCGGCGCGGCTGGACGCGGTATCGATGATCTTC ++ +AA>EF8EIFFGFGECGEFHFFFGFFGFFFGEFGFGFGFF +@HS21_09876:2:1211:5990:82312#83 +TTTTCGGTCACCGCGGTGCGCAACCTGCACCCGGTGACCCTCTC ++ +HGFEH0FFDDDGCF7GFD1GCFGFGGFGFFGHEFF?FFFEEDEE +@HS21_09876:2:2103:19946:55809#83 +GGGTCATAACGCCGCGGAGATTCTCTCGCGCGGTCAGCAGAAGC ++ +HHEAE'EFFEGGGFHEFAHGFHG@GEFHFEGFGFFFFAGGFFF;>DFG=EDF:GHHEG6GGDGFFFFGGF6FFEFGC1BFF diff -Nru bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/smallref.fa bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/smallref.fa --- bio-tradis-1.4.1+dfsg/t/data/RunTradisTaglessSmalt/smallref.fa 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/data/RunTradisTaglessSmalt/smallref.fa 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,165 @@ +>AE004091 AE004091.2 Pseudomonas aeruginosa PAO1, complete genome. +tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat +gacgtaatagatagatacaaggaagtcatttttcttttaaaggatagaaacggttaatgc +tcttgggacggcgcttttctgtgcataactcgatgaagcccagcaattgcgtgtttctcc +ggcaggcaaaaggttgtcgagaaccggtgtcgaggctgtttccttcctgagcgaagcctg +gggatgaacgagatggttatccacagcggttttttccacacggctgtgcgcagggatgta +cccccttcaaagcaagggttatccacaaagtccaggacgaccgtccgtcggcctgcctgc +ttttattaaggtcttgatttgcttggggcctcagcgcatcggcatgtggataagtccggc +ccgtccggctacaataggcgcttatttcgttgtgccgcctttccaatctttgggggatat +ccgtgtccgtggaactttggcagcagtgcgtggatcttctccgcgatgagctgccgtccc +aacaattcaacacctggatccgtcccttgcaggtcgaagccgaaggcgacgaattgcgtg +tgtatgcacccaaccgtttcgtcctcgattgggtgaacgagaaatacctcggtcggcttc +tggaactgctcggtgaacgcggcgagggtcagttgcccgcgctttccttattaataggca +gcaagcgtagccgtacgccgcgcgccgccatcgtcccatcgcagacccacgtggctcccc +cgcctccggttgctccgccgccggcgccagtgcagccggtatcggccgcgcccgtggtag +tgccacgtgaagagctgccgccagtgacgacggctcccagcgtgtcgagcgatccctacg +agccggaagaacccagcatcgatccgctggccgccgccatgccggctggagcagcgcctg +cggtgcgcaccgagcgcaacgtccaggtcgaaggtgcgctgaagcacaccagctatctca +accgtaccttcaccttcgagaacttcgtcgagggcaagtccaaccagttggcccgcgccg +ccgcctggcaggtggcggacaacctcaagcacggctacaacccgctgttcctctacggtg +gcgtcggtctgggcaagacccacctgatgcatgcggtgggcaaccacctgctgaagaaga +acccgaacgccaaggtggtctacctgcattcggaacgtttcgtcgcggacatggtgaagg +ccttgcagctcaacgccatcaacgaattcaagcgcttctaccgctcggtggacgcactgt +tgatcgacgacatccagttcttcgcccgtaaggagcgctcccaggaggagttcttccaca +ccttcaatgcccttctcgaaggcggccagcaggtgatcctcaccagcgaccgctatccga +aggaaatcgaaggcctggaagagcggctgaaatcccgcttcggctggggcctgacggtgg +ccgtcgagccgccggaactggaaacccgggtggcgatcctgatgaagaaggccgagcagg +cgaagatcgagctgccgcacgatgcggccttcttcatcgcccagcgcatccgttccaacg +tgcgtgaactggaaggtgcgctgaagcgggtgatcgcccactcgcacttcatgggccggc +cgatcaccatcgagctgattcgcgagtcgctgaaggacctgttggcccttcaggacaagc +tggtcagcatcgacaacatccagcgcaccgtcgccgagtactacaagatcaagatatccg +atctgttgtccaagcggcgttcgcgctcggtggcgcgcccgcgccaggtggccatggcgc +tctccaaggagctgaccaaccacagcctgccggagatcggcgtggccttcggcggtcggg +atcacaccacggtgttgcacgcctgtcgtaagatcgctcaacttagggaatccgacgcgg +atatccgcgaggactacaagaacctgctgcgtaccctgacaacctgacgcagcccacgag +gcaagggactagaccatgcatttcaccattcaacgcgaagccctgttgaaaccgctgcaa +ctggtcgccggcgtcgtggaacgccgccagacattgccggttctctccaacgtcctgctg +gtggtcgaaggccagcaactgtcgctgaccggcaccgacctcgaagtcgagctggttggt +cgcgtggtactggaagatgccgccgaacccggcgagatcaccgtaccggcgcgcaagctg +atggacatctgcaagagcctgccgaacgacgtgctgatcgacatccgtgtcgaagagcag +aaacttctggtgaaggccgggcgtagccgcttcaccctgtccaccctgccggccaacgat +ttccccaccgtagaggaaggtcccggctcgctgaacttcagcattgcccagagcaagctg +cgtcgcctgatcgaccgcaccagcttcgccatggcccagcaggacgtgcgttactacctc +aacggcatgctgctggaagtgaacggcggcaccctgcgctccgtcgccaccgacggccac +cgactggccatgtgctcgctggatgcgcagatcccgtcgcaggaccgccaccaggtgatc +gtgccgcgcaaaggcatcctcgaactggctcgtctgctcaccgagcaggacggcgaagtc +ggcatcgtcctgggccagcaccatatccgtgccaccactggcgaattcaccttcacttcg +aagctggtggacggcaagttcccggactacgagcgtgtactgccgcgcggtggcgacaag +ctggtggtcggtgaccgccagcaactgcgcgaagccttcagccgtaccgcgatcctctcc +aacgagaagtaccgcggcattcgcctgcagctttccaacggtttgctgaaaatccaggcg +aacaacccggagcaggaagaggccgaggaagaagtgcaggtcgagtacaacggcggcaac +ctggagataggcttcaacgtcagttacctgctcgacgtgctgggtgtgatcggtaccgag +caggtccgcttcatcctttccgattccaacagcagcgccctggtccacgaggccgacaat +gacgattctgcctatgtcgtcatgccgatgcgcctctaaacatactgaatgtccctgacc +cgcgtttcggtcaccgcggtgcgcaacctgcacccggtgaccctctccccctccccccgc +atcaacatcctctacggcgacaacggcagcggcaagaccagcgtgctcgaagccatccac +ctgctgggcctggcgcgttcattccgcagtgcgcgcttgcagccggtgatccagtatgag +gaagcggcctgcaccgtattcggccaggtgatgttggccaacggcatcgccagcaacctg +gggatttcccgtgagcgccagggcgagttcaccatccgcatcgatgggcagaacgcccgg +agtgcggctcaattggcggaaactctcccactgcaactgatcaacccggacagctttcgg +ttgctcgagggagcgccgaagatccggcgacagttcctcgattggggagtgttccacgtg +gaacctcggtttctgcccgtctggcagcgcctgcagaaggcgctgcgccagcggaactcc +tggctccggcatggtaaactggaccccgcgtcgcaagcggcctgggaccgggaattgagc +ctggccagcgatgagatcgatgcctaccgcagaagctatatccaggcgttgaaaccggta +ttcgaggaaacactcgccgaattggtttcactggatgacctgacccttagctactaccga +ggctgggacaaggaccgggacctcctggaggttctggcttccagcctgttgcgcgaccag +cagatgggccacacccaggcgggaccgcagcgtgcggatcttcgcatacggttggcaggt +cataacgccgcggagattctctcgcgcggtcagcagaagctggtggtatgcgccctgcgc +atcgcccaaggccatctgatcaatcgcgccaagcgcggacagtgcgtctacctggtggac +gacctgccctcggaactggatgagcagcatcgaatggctctttgccgcttgcttgaagat +ttgggttgccaggtattcatcacctgcgtggacccgcaactattgaaagacggctggcgc +acggatacgccggtatccatgttccacgtggaacatggaaaagtctctcagaccacgacc +atcgggagtgaagcatgagcgagaacaacacgtacgactcttccagcatcaaggtgctga +aggggctggatgccgtacgcaagcgccccggcatgtacatcggcgacaccgacgatggca +ccggtctgcaccacatggtgttcgaggtggtggataactccatcgacgaagcgctggccg +gttactgcagcgaaatcagcatcaccatccatacggatgagtcgatcactgtccgcgaca +atggacgcggtattccggtggatatccacaaggaagaaggggtttctgcggcggaagtga +tcatgaccgtcctccacgccggcggcaagttcgacgacaacacctacaaggtgtccggcg +gcttgcacggtgtgggcgtctcggtggtgaacgcgctgtcccatgaactacgcctgacca +tccgtcgccacaacaaggtctgggaacaggtctaccaccacggcgttccgcagttcccac +tgcgcgaagtgggcgagaccgatggctccggcaccgaagttcacttcaagccgtccccgg +agaccttcagcaacatccacttcagttgggacatcctggccaagcgcatccgcgagctgt +ccttcctcaactccggcgtcggcatcctgctgcgcgacgagcgtaccggcaaggaggagc +tgttcaagtacgaaggcggtctgaaggccttcgtcgagtacctgaacaccaacaagaccg +cggtgaacgaggtattccacttcaacgtccagcgtgaagaggacggcgtgggtgtggaag +tcgccttgcagtggaacgacagcttcaacgagaacctgctctgcttcaccaacaacatcc +cgcagcgtgacggcggcacccacctggccggtttccgttcggcgctgacgcgtaacctga +acaactacatcgaggccgaaggcctggcgaagaagttcaagatcgccaccaccggcgacg +atgcccgcgaaggcctcaccgcgatcatctcggtgaaggtaccggacccgaagttcagct +cgcagaccaaggacaagctggtctcctccgaggtgaagactgcggtggaacaggagatgg +gcaagtacttcgccgacttcctgctggagaatcccaacgaagccaaggccgtggtcggca +agatgatcgacgccgcccgtgcccgcgaggccgcgcgcaaggcgcgcgagatgacccgcc +gcaagggcgcgctggacatcgccggcctgcccggcaaactggccgattgccaggaaaagg +acccggcgctctccgaactgtacatcgtggagggtgactccgcgggcggttccgccaagc +agggccgcaatcgccggacccaggcgatcctgccgctcaagggcaagatcctcaacgtcg +aaaaggcgcgcttcgacaagatgctctcctcccaggaggtcggtacgctgatcaccgccc +tgggctgtggcatcggccgcgaggaatacaacatcgacaagctgcgctaccacaacatca +tcatcatgaccgatgctgacgtcgacggttcgcacatccgcaccctgctgttgaccttct +tcttccgccagatgcccgagctgatcgagcgtggctacatctacatcgcccagcccccgt +tgtacaaggtcaagcgcggcaagcaggagcagtacatcaaggacgaccaggccatggaag +agtacatgacccagtcggccctggaagacgccagcctgcacgtcaacgagcacgctccgg +gcctgtccggggcggcgctggagaaactggtcaacgagtatcgcggggtgatcgccaccc +tcaagcgcctgtcgcgcctgtacccccaggagctgaccgagcacttcatctacctgccta +ccgtgtcggtggacgacctggctaacgagtcggccatgcagggctggttggagaagttcc +aggcgcgcctgaccgccgccgagaagtccggcctgacctacaaggccagcctgcgcgaag +accgcgagcgccacctgtggctgcccgaggtggaactggtggcccacggcctgtccagct +acgtcaccttcaaccgtgacttcttcgccagcaatgactaccgctcggtgtcgctgctcg +gcgaccagctgaacagcctgctggaagacggcgcctacgtgcagaagggtgagcgcaagc +gcccgatcagcgccttcaaggacggcctggactggctgatggccgaaggtaccaagcgcc +acagcatccagcgatacaaggggctgggcgagatgaaccctgagcagctgtgggaaacca +ccatggatccgaacgtccggcgcatgctcaaggtgaccatcgaggatgccatcgccgccg +accagatcttcaacaccctgatgggcgatgccgtggagccgcgccgcgacttcatcgaaa +gcaacgcgctggcggtgtcgaacctggacgtgtgacaggtcggcagaccgaccctcatgg +aaaccccggcctggcgccggggttttctttttgcgccaggtagcctggatacgggcgcca +ggggtgccttgccaaggtgtggccgagccccggttactcgccggcattggcaccctggac +ccgggcctcctggcggcgtggcaccgcttctgtgggcagcggtcgccggtcggttcggtc +gatcgttgccagccggccttgctttgcgcctcgcgtgaaaacaagaagccccgctatggc +ggggcttcttttatcgaatcggcgcacagtacgccttgcagggggctttgcggcccttca +cgagaccaccgacggctccggatggctgacccgctgctggatggggctgatctcggccat +ggtctcgctgacccaggcttcggcgcgctggtttagctcggcgatggcgcgcgggccttc +gccttcggcgtgcatggccgggccgatcaccacctggatggtgcccgggtacttggccca +gccggccttgggccaatactgcccggcgttgtgggcgatcggcagtaccggtagcccggc +gttgaccgccagggcggtgccgccgcgggagaacttgcccatctgccccaccggaatacg +cgtgccttccgggaagatcagcacccaggcgcctttcttcaggcactcgtcgccctgctt +ggccagttgcttgagggccagcttgggctggctgcggtcgatggcgatgggcttgagcag +ggccagggcccagccgaagaacggcacgtagagcagctcgcgcttgagtacctggctgag +tggctcgaagaagccggagaggaagaaggtttcccaggtgctctggtgcttggagaggat +cacgcagggcttttccgggatgttctccagtccgcgcacctcgtagcggatgccggcgac +cacgcgggtcagccagatcgcgaagcggcaccagttctgtaccacgaagcggtagcgggc +gcggaacggcaggatcggcgcgatgaagaagctgagggtgccccagacgaacgcgctggc +ggacagcagcaggtaaaagaggacggttctgatggcctgcactgtcgacatgtattctga +ccttactgaagtaatgcgctggcgactgccgccagatcgtcgaatatcagggtgccctct +ggcaagggcttgcccagcgtacgtacaccttttccggtctttaccaataccggctgacaa +tcgacggcccgcgccgcctccaggtcaccgatgctgtcgccgacgaaccagatacccgac +agatcgaccccgtagtgctcgccgatctgccgcagcatacccggcttcggcttgcggcag +tcgcaaccgtcgtccggtccatgcggacaatagacgatgaggccgacctcgccgccctgc +tccgcgaccagttcgcgcaagcgcgcatgcatggcctcgagcactgccaggtcgtaatag +ccacgggcgatgccggactggttggtagccaccgcgacggtccagccggcctggctcagg +cgggcgatggcctcgatcgagctggggatggggatccactcgtcgagggtcttgatgtaa +tcgtcggagtcgaggttgatgactccatcgcggtcgagaatcagcagggaacgggacatc +gatgcgcagttggccatgaacggaaaggatcgattctacctcagccagccggagcatcgc +ggatggatcgacgagccccctacgctggacaatctgtactagattcaataatggcaatgg +aatggcaatcccaggccagggagtcatttggcacgcagcagtgggtgtctcggagtacgt +gcgaaccccttggcgggtggatcaccggagtaacgcagtaagcgcctatcgcatgccagc +acggccgaccggccgtgtttccaccacaggtggagcgggcgtgacgacggggagttccgg +ggcgtctgcccgttcccaaggacggtaaccgtgaaacgcctgaaaaagacactgcacctt +tcaagcttgtccctcgcttccctggctctttcttccgccgccctggcggccgctccggtc +atgctcgaccagggcaaggaatggaccgaaagccaccgccaggacttctacagccgcgac +cagggctcgcaggtgatgcccctgccctggctcaaggcgttgcgacagccggatggaacg +cctttcctcgccgacagcctggcccgctacggctatttgcccaaccccaaggcgcccgcg +gaaggcctgccggtgggcttcaccgtagccggcacgggcgcccggcagatggtcggcatg +acctgttcggcctgccatacccggcagatcgaggtgaagggcactgcctatcggatcgac +ggcggtccggcgatcgtcgacttccaggcattcctcgccgacctcgatcgggccgtggga +ccgctgaccagcgatgacgccgccttcgacgccttcgccaagccgatcctcggggccaat +ccgcctcccggtgcgcgcgacgctctgctcgcggcggtgaaggaatggtacgagccctat +cacacgctgatcgagcgcgcgctgcccaaggacacctggggaccggcgcggctggacgcg +gtatcgatgatcttcaaccgccttaccgggctggatatcggcaccgcgccgccctacctg +attcccgacaacatcaaggcggccgatgcgccggtgcgctatccgttcctgtggaacgcg +gcgcggcagaacaagacccagtggcccggcttcgccgccaacggcaacgacctgctcggc +ctggcgcgcaatgtcggcgaggtctacggggtgttcgccaccttccacccgcagaagagc +aagttccacctgctgggcatggactacctgaagatcaactcggccaacttccacgggctg +ggcaagctggaagacctgatcaagaagatcggcccgccgaagtggccctgggcggtggac +aagcacctggccaggaaaggcgcgctgatcttcgcccgcaagaccgacgaaggtggctgc +gtggagtgccacggcatccggatcaaggacctggtgctttgggacactccgctgagggac +gtcggcagcgacagccgccagcacgccatcctcgatggccaggtgcagaccggcgtgatg diff -Nru bio-tradis-1.4.1+dfsg/t/requires_external.t bio-tradis-1.4.5+dfsg2/t/requires_external.t --- bio-tradis-1.4.1+dfsg/t/requires_external.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/t/requires_external.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,9 @@ +#!/usr/bin/env perl + +use Test::Most; +plan tests => 6; +bail_on_fail if 0; +use Env::Path 0.18 'PATH'; + +ok(scalar PATH->Whence($_), "$_ in PATH") for qw(awk samtools gunzip gzip smalt tabix); + diff -Nru bio-tradis-1.4.1+dfsg/.travis.yml bio-tradis-1.4.5+dfsg2/.travis.yml --- bio-tradis-1.4.1+dfsg/.travis.yml 2018-09-20 14:56:44.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/.travis.yml 1970-01-01 00:00:00.000000000 +0000 @@ -1,16 +0,0 @@ -language: perl -addons: - apt: - packages: - - zlib1g-dev -perl: - - "5.14" -sudo: false -install: - - "source ./install_dependencies.sh" -before_script: - - cpanm --quiet --notest Dist::Zilla::App::Command::cover - - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov -script: "dzil test" -after_success: - - dzil cover -test -report codecov \ No newline at end of file diff -Nru bio-tradis-1.4.1+dfsg/xt/author/00-compile.t bio-tradis-1.4.5+dfsg2/xt/author/00-compile.t --- bio-tradis-1.4.1+dfsg/xt/author/00-compile.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/xt/author/00-compile.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,129 @@ +use 5.006; +use strict; +use warnings; + +# this test was generated with Dist::Zilla::Plugin::Test::Compile 2.058 + +use Test::More; + +plan tests => 35; + +my @module_files = ( + 'Bio/Tradis.pm', + 'Bio/Tradis/AddTagsToSeq.pm', + 'Bio/Tradis/Analysis/Exceptions.pm', + 'Bio/Tradis/Analysis/InsertSite.pm', + 'Bio/Tradis/CombinePlots.pm', + 'Bio/Tradis/CommandLine/AddTags.pm', + 'Bio/Tradis/CommandLine/CheckTags.pm', + 'Bio/Tradis/CommandLine/FilterFastqTags.pm', + 'Bio/Tradis/CommandLine/PlotCombine.pm', + 'Bio/Tradis/CommandLine/PlotTradis.pm', + 'Bio/Tradis/CommandLine/RemoveFastqTags.pm', + 'Bio/Tradis/CommandLine/RunMapping.pm', + 'Bio/Tradis/CommandLine/TradisAnalysis.pm', + 'Bio/Tradis/CommandLine/TradisBam.pm', + 'Bio/Tradis/DetectTags.pm', + 'Bio/Tradis/Exception.pm', + 'Bio/Tradis/FilterTags.pm', + 'Bio/Tradis/Map.pm', + 'Bio/Tradis/Parser/Bam.pm', + 'Bio/Tradis/Parser/Cigar.pm', + 'Bio/Tradis/Parser/Fastq.pm', + 'Bio/Tradis/RemoveTags.pm', + 'Bio/Tradis/RunTradis.pm', + 'Bio/Tradis/Samtools.pm', + 'Bio/Tradis/TradisPlot.pm' +); + +my @scripts = ( + 'bin/add_tradis_tags', + 'bin/bacteria_tradis', + 'bin/check_tradis_tags', + 'bin/combine_tradis_plots', + 'bin/filter_tradis_tags', + 'bin/remove_tradis_tags', + 'bin/tradis_gene_insert_sites', + 'bin/tradis_merge_plots', + 'bin/tradis_plot' +); + +# no fake home requested + +my @switches = ( + -d 'blib' ? '-Mblib' : '-Ilib', +); + +use File::Spec; +use IPC::Open3; +use IO::Handle; + +open my $stdin, '<', File::Spec->devnull or die "can't open devnull: $!"; + +my @warnings; +for my $lib (@module_files) +{ + # see L + my $stderr = IO::Handle->new; + + diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } + $^X, @switches, '-e', "require q[$lib]")) + if $ENV{PERL_COMPILE_TEST_DEBUG}; + + my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-e', "require q[$lib]"); + binmode $stderr, ':crlf' if $^O eq 'MSWin32'; + my @_warnings = <$stderr>; + waitpid($pid, 0); + is($?, 0, "$lib loaded ok"); + + shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ + and not eval { +require blib; blib->VERSION('1.01') }; + + if (@_warnings) + { + warn @_warnings; + push @warnings, @_warnings; + } +} + +foreach my $file (@scripts) +{ SKIP: { + open my $fh, '<', $file or warn("Unable to open $file: $!"), next; + my $line = <$fh>; + + close $fh and skip("$file isn't perl", 1) unless $line =~ /^#!\s*(?:\S*perl\S*)((?:\s+-\w*)*)(?:\s*#.*)?$/; + @switches = (@switches, split(' ', $1)) if $1; + + close $fh and skip("$file uses -T; not testable with PERL5LIB", 1) + if grep { $_ eq '-T' } @switches and $ENV{PERL5LIB}; + + my $stderr = IO::Handle->new; + + diag('Running: ', join(', ', map { my $str = $_; $str =~ s/'/\\'/g; q{'} . $str . q{'} } + $^X, @switches, '-c', $file)) + if $ENV{PERL_COMPILE_TEST_DEBUG}; + + my $pid = open3($stdin, '>&STDERR', $stderr, $^X, @switches, '-c', $file); + binmode $stderr, ':crlf' if $^O eq 'MSWin32'; + my @_warnings = <$stderr>; + waitpid($pid, 0); + is($?, 0, "$file compiled ok"); + + shift @_warnings if @_warnings and $_warnings[0] =~ /^Using .*\bblib/ + and not eval { +require blib; blib->VERSION('1.01') }; + + # in older perls, -c output is simply the file portion of the path being tested + if (@_warnings = grep { !/\bsyntax OK$/ } + grep { chomp; $_ ne (File::Spec->splitpath($file))[2] } @_warnings) + { + warn @_warnings; + push @warnings, @_warnings; + } +} } + + + +is(scalar(@warnings), 0, 'no warnings found') + or diag 'got warnings: ', ( Test::More->can('explain') ? Test::More::explain(\@warnings) : join("\n", '', @warnings) ); + + diff -Nru bio-tradis-1.4.1+dfsg/xt/author/pod-syntax.t bio-tradis-1.4.5+dfsg2/xt/author/pod-syntax.t --- bio-tradis-1.4.1+dfsg/xt/author/pod-syntax.t 1970-01-01 00:00:00.000000000 +0000 +++ bio-tradis-1.4.5+dfsg2/xt/author/pod-syntax.t 2019-12-04 14:40:22.000000000 +0000 @@ -0,0 +1,7 @@ +#!perl +# This file was automatically generated by Dist::Zilla::Plugin::PodSyntaxTests. +use strict; use warnings; +use Test::More; +use Test::Pod 1.41; + +all_pod_files_ok();