.gitattributes

-.bam filter=lfs diff=lfs merge=lfs -text
-samples/sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text
-sample_lg_tr.bam filter=lfs diff=lfs merge=lfs -text

.gitignore

-blib/
-.build/
-_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

.travis.yml

-sudo: required
-services:
-  - docker
-install:
-  - docker pull sangerpathogens/bio-tradis
-script:
-  - docker run --rm -it sangerpathogens/bio-tradis /bin/bash -c "git clone https://github.com/sanger-pathogens/Bio-Tradis.git && cd Bio-Tradis && dzil test"

MANIFEST

+# 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
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+t/data/RunTradisSmalt/notags.fastq
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+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

META.yml

+---
+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 <path-help@sanger.ac.uk>'
+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:
+    -
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+      name: MetaResources
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+              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'

Makefile.PL

+# 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 <path-help\@sanger.ac.uk>",
+  "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);

README

+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 <path-help@sanger.ac.uk>
+
+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
+

bin/add_tradis_tags

 #!/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' ) }
@@ -20,3 +16,35 @@ 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 <path-help@sanger.ac.uk>
+
+=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

bin/bacteria_tradis

 #!/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
 
-=head1 SYNOPSIS
-
-Take a fastq, reference and a tag and generates insertion
-site plots for use in Artemis
-
-=cut
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
@@ -23,3 +17,36 @@ 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
+
+=head1 AUTHOR
+
+Carla Cummins <path-help@sanger.ac.uk>
+
+=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

bin/check_tradis_tags

 #!/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' ) }
@@ -20,3 +16,35 @@ 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 <path-help@sanger.ac.uk>
+
+=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

bin/combine_tradis_plots

 #!/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
 
-=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
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
@@ -23,3 +17,37 @@ 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.
+
+=head1 AUTHOR
+
+Carla Cummins <path-help@sanger.ac.uk>
+
+=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

bin/filter_tradis_tags

 #!/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
 
-=head1 SYNOPSIS
-
-Checks tags at the start of the fastq sequence and returns a file containing those that
-match the tag provided
-
-=cut
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
@@ -21,3 +16,36 @@ 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
+
+=head1 AUTHOR
+
+Carla Cummins <path-help@sanger.ac.uk>
+
+=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

bin/remove_tradis_tags

 #!/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' ) }
@@ -20,3 +16,35 @@ 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 <path-help@sanger.ac.uk>
+
+=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

bin/tradis_gene_insert_sites

 #!/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;
@@ -328,3 +308,51 @@ sub output_header
 {
   ['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 <path-help@sanger.ac.uk>
+
+=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

bin/tradis_merge_plots

 #!/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;
@@ -97,3 +79,49 @@ for my $library_name (keys %coverage_plots)
     }
   }
 }
+
+__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 <path-help@sanger.ac.uk>
+
+=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

bin/tradis_plot

 #!/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' ) }
@@ -21,3 +16,36 @@ 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 <path-help@sanger.ac.uk>
+
+=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

debian/changelog

-bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium
+bio-tradis (1.4.5+dfsg2-1) UNRELEASED; urgency=medium
 
   * Team upload.
   * debian/patches/samtools1.10: remove version parsing code that can't handle
     samtools version 1.10
+  * Switch to cpan for the source
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 25 Dec 2019 13:28:31 +0100
 

debian/control

@@ -4,32 +4,22 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: perl
 # Testsuite: autopkgtest-pkg-perl
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
-               libtext-csv-perl,
-               samtools,
-               smalt,
-               tabix,
-               bwa,
-               libtrycatch-perl,
-               libtest-most-perl,
-               libtest-files-perl,
-               libbio-perl-perl,
-               dh-dist-zilla,
-               libdist-zilla-plugin-checkextratests-perl,
-               libdist-zilla-plugin-requiresexternal-perl,
-               libdist-zilla-plugin-git-perl,
-               libdist-zilla-plugin-podweaver-perl,
-               libdist-zilla-role-pluginbundle-pluginremover-perl,
-               libdist-zilla-plugin-test-compile-perl,
-               libdist-zilla-plugin-modulebuildtiny-fallback-perl,
-               libdist-zilla-config-slicer-perl,
-               libtest-file-sharedir-perl,
-               libdist-zilla-plugin-modulebuildtiny-perl,
-               libdist-zilla-plugin-readmefrompod-perl,
-               libdist-zilla-plugin-makemaker-awesome-perl,
-               libtest-pod-perl,
-               libdist-zilla-plugin-test-reportprereqs-perl,
-               libdist-zilla-plugin-metaprovides-package-perl
+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
@@ -37,8 +27,13 @@ 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,