New upstream version 1.4.5+dfsg2 (a7a3476c) · Commits · Debian Med / bio-tradis

.gitattributes

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		.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

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		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

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		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"

LICENSE

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MANIFEST

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		# 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