| Next changeset 1:e1b47f2236b6 (2016-06-06) |
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Commit message:
Initial upload |
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added:
snippy.xml test-data/Ecoli.fna test-data/reads_1.fq test-data/reads_2.fq test-data/test/snps.aligned.fa test-data/test/snps.bed test-data/test/snps.consensus.fa test-data/test/snps.csv test-data/test/snps.depth.gz test-data/test/snps.depth.gz.tbi test-data/test/snps.gff test-data/test/snps.html test-data/test/snps.log test-data/test/snps.tab test-data/test/snps.txt test-data/test/snps.vcf test-data/test/snps.vcf.gz test-data/test/snps.vcf.gz.tbi tool_dependencies.xml |
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| diff -r 000000000000 -r 0801bffdfcc8 snippy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy.xml Sun Jun 05 21:12:39 2016 -0400 |
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| b'@@ -0,0 +1,159 @@\n+<tool id="snippy" name="snippy" version="0.2.0">\n+ <requirements>\n+ <requirement type="package" version="3.0">snippy</requirement>\n+ <requirement type="package" version="1.2">samtools</requirement>\n+ <requirement type="package" version="0.9.20">freebayes</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+\n+ <command><![CDATA[\n+ cp $ref foo.fna &&\n+ snippy\n+ --outdir out\n+ --cpus "\\${GALAXY_SLOTS:-1}"\n+ --ref foo.fna\n+ $cleanup\n+ #if str( $advanced.is_advanced ) == "advanced"\n+ --mapqual $advanced.mapqual\n+ --mincov $advanced.mincov\n+ --minfrac $advanced.minfrac\n+ #if $advanced.rgid\n+ --rgid $advanced.rgid\n+ #end if\n+ #if $advanced.bwaopt\n+ --bwaopt $advanced.bwaopt\n+ #end if\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired"\n+ --pe1 $fastq_input.fastq_input1\n+ --pe2 $fastq_input.fastq_input2\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired_collection"\n+ --pe1 $fastq_input.fastq_input1.forward\n+ --pe2 $fastq_input.fastq_input1.reverse\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "single"\n+ --se $fastq_input.fastq_input1\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired_iv"\n+ --peil $fastq_input.fastq_input1\n+ #end if\n+\n+ &&\n+\n+ gunzip out/snps.depth.gz\n+\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">\n+ <option value="paired">Paired</option>\n+ <option value="single">Single</option>\n+ <option value="paired_collection">Paired Collection</option>\n+ <option value="paired_iv">Paired Interleaved</option>\n+ </param>\n+ <when value="paired">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>\n+ <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>\n+ </when>\n+ <when value="single">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>\n+ </when>\n+ <when value="paired_collection">\n+ <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>\n+ </when>\n+ <when value="paired_iv">\n+ <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>\n+ </when>\n+ </conditional>\n+ <param name="cleanup" type="boolean" checked="true" truevalue="--cleanup" falsevalue="" label="Cleanup the non-snp output files" help="Remove all non-SNP files: BAMs, indices etc" />\n+ <conditional name="advanced">\n+ <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings">\n+ <option value="advanced">Show advanced settings</option>\n+ <option value="simple" selected="true">Hide advanced settings</option>\n+ </param>\n+ <when value="advanced">\n+ <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />\n+ <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />\n+ <param name="'..b'der @RG ID" help="Use this @RG ID: in the BAM header" />\n+ <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />\n+ </when>\n+ <when value="simple">\n+\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>\n+ <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>\n+ <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>\n+ <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>\n+ <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>\n+ <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>\n+ <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>\n+ <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>\n+ <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">\n+ <filter>cleanup is False</filter>\n+ </data>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="ref" value="Ecoli.fna" ftype="fasta" />\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />\n+ <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />\n+ <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />\n+ </test>\n+ </tests>\n+\n+\n+ <help><![CDATA[\n+ This is a change to force a reinstall\n+ Synopsis:\n+ snippy 3.0 - fast bacterial variant calling from NGS reads\n+Author:\n+ Torsten Seemann <torsten.seemann@gmail.com>\n+Usage:\n+ snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>\n+ snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>\n+ snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>\n+Options:\n+ --help This help\n+ --version Print version and exit\n+ --citation Print citation for referencing snippy\n+ --quiet No screen output (default OFF)\n+ --cpus [N] Maximum number of CPU cores to use (default \'8\')\n+ --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default \'\')\n+ --outdir [X] Output folder (default \'\')\n+ --prefix [X] Prefix for output files (default \'snps\')\n+ --force Force overwrite of existing output folder (default OFF)\n+ --pe1|R1|left [X] Reads, paired-end R1 (left) (default \'\')\n+ --pe2|R2|right [X] Reads, paired-end R2 (right) (default \'\')\n+ --se|single [X] Single-end reads (default \'\')\n+ --peil [X] Reads, paired-end R1/R2 interleaved (default \'\')\n+ --mapqual [n.n] Minimum mapping quality to allow (default \'60\')\n+ --mincov [N] Minimum coverage of variant site (default \'10\')\n+ --minfrac [n.n] Minumum proportion for variant evidence (default \'0.9\')\n+ --report Produce long report with visual alignment (slow) (default OFF)\n+ --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)\n+ --rgid [X] Use this @RG ID: in the BAM header (default \'\')\n+ --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default \'\')\n+\n+ ]]></help>\n+\n+ <citations>\n+ <citation type="bibtex">@UNPUBLISHED{Seemann2013,\n+ author = "Seemann T",\n+ title = "snippy: fast bacterial variant calling from NGS reads",\n+ year = "2015",\n+ note = "https://github.com/tseemann/snippy"}\n+ </citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/Ecoli.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Ecoli.fna Sun Jun 05 21:12:39 2016 -0400 |
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| b'@@ -0,0 +1,78551 @@\n+>gi|15829254|ref|NC_002695.1| Escherichia coli O157:H7 str. Sakai, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCACCACCATCACCATTACCATTACCACAGGTAACGGTGCGGGCTGACGCGTAC\n+AGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACA\n+ACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATA\n+TTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCA\n+CCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGT\n+ATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGCCGGGATTCCCGCTGGCGCAATTGAAAACTT\n+TCGTCGACCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTAGGGCAGTGCCCGGA\n+TAGCATTAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAA\n+GCGCGCGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAAT\n+CTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCT\n+GATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTACTTGGACGCAACGGTTCCGACTAC\n+TCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTAT\n+ATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAATCGATGTCCTACCAGGAAGCGATGGA\n+GCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCT\n+TGCCTGATTAAAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGTCGTGATGAAGACG\n+AATTACCGGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAA\n+AGGAATGGTCGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGCCCGTATTTCCGTGGTGCTGATT\n+ACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTCCGCAAAGCGACTGTGTGCGAGCTGAACGGG\n+CAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGGCT\n+GGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCG\n+CTGGCCCGCGCCAATATCAACATTGTCGCTATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGG\n+TAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTAT\n+CGAAGTGTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGC\n+TGGTTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCTAACTCGAAGGCTCTGCTCACCAATG\n+TGCATGGCCTAAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCG\n+CTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACCTCCAGCCAGGCA\n+GTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACA\n+CCTCGTCGATGGATTACTACCATCTGTTGCGTCATGCGGCTGAAAAATCGCGGCGTAAATTCCTCTATGA\n+CACCAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCTGGTGATGAATTG\n+ATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTT\n+TCTCCGAGGCGACTACGCTGGCGCGGGAAATGGGTTATACCGAACCGGATCCGCGAGATGATCTTTCTGG\n+TATGGATGTAGCGCGTAAACTATTAATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATT\n+GAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCTGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGT\n+CACAGCTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGT\n+TGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTC\n+AAAGTGAAAAATGGCGAAAACGCCCTGGCCTTTTATAGCCACTATTATCAGCCGCTGCCGTTGGTGCTGC\n+GCGGATATGGTGCGGGCAATGACGTTACCGCTGCCGGTGTCTTTGCCGATCTGCTACGTACCCTCTCATG\n+GAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGA\n+TGTGCTCGGGGCGGCGGTGACACCCGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGTCGGCA\n+GAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCG\n+TTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTGGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAA\n+GAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCTCTGATGGCGATGAAT\n+GAACACTGCGGCAAGCCGCTTAATGACACCCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCT\n+CCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAA\n+CGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAA\n+GTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGC\n+GACACTTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGA\n+TGTTATCGCAGAACCCTACCGTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAA\n+ATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTTGCTCTGTGTGACAAGCCGGATA\n+CCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTG\n+CCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTTAAAGATCACAAT\n+GAGCAG'..b'GAGGTTAACGTTGCTG\n+CTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCAAGAG\n+CGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGT\n+GGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAA\n+AAAGCAGCGGTCTGGGGTTGGCGTTTGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCG\n+CAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGGCTTCACCGTCACTTCACATAGCTTCAAATTCTT\n+CCCACATAGCCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGA\n+AAATGACCACCCTGTTTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGATTCGGCAGGTGATTGT\n+CGAACGTGCCGATTACCGTAGCGATGTGGAAGATGCGATTCGCCAAAGTACCAGCGGGCCGCAAAAACTC\n+GTTGGGCCTCTTATCGCTATTCCTGTGACCGAGCTTTATACGGTGCAGGAAGAGGATAAAACCGTGGAGC\n+GGAAACGAAGTTTTATCCATTTTTGGTTACCTGAGTCATTGATGGTTGATGGCAATCAGAACGTGGAAGA\n+ACGCAAGATAGGGATTTATACCGGTCAGGTCTGGCACAGTGATTTAACGCTAAAAGCCGATTTCGATGTT\n+TCGCGTCTTAGCGAACTCGACGCGCCAAATATCACCTTTGGCAAGCCATTTATTGTGATTAGCGTCGGGG\n+ATGCGCGTGGTATTGGTGTGGTGAAAGCGCCTGAAGTTAACGGAACGGCGCTGACTATTGAACCCGGCAT\n+CGGGTTAGAGCAAGGCGGGCAGGGCGTGCATATCCCTTTACCCGAAGGGGACTGGCGGAAGCAGAACCTG\n+AAGCTGAATATGGCACTGAATTTAAGCGGTACCGGCGATCTTTCTGTGGTGCCTGCGGGGCGTAATAGCG\n+AAATGACCTTAACCAGCAACTGGCCGCATCCCAGTTTTTTAGGTGATTTTCTACCAGCCAAACGGGAAGT\n+TAGTGAGTCAGGTTTTCAGGCGCAATGGCAAAGCAGCTGGTTTGCTAATAATCTCGGTGAGCGTTTTGCT\n+TCAGGCAATGATACCGGCTGGGAAAACTTCCCCGCGTTTAGCGTCGCAGTGACGACGCCCGCCGATCAAT\n+ACCAATTAACTGACCGGGCGACTAAGTATGCCATTCTGCTGATTGCGCTGACTTTTATGGCGTTCTTTGT\n+TTTTGAAACGCTCACCGCGCAACGTTTACACCCAATGCAATATTTGCTGGTGGGGCTTTCATTGGTGATG\n+TTTTATTTGCTCTTGCTGGCGCTTTCTGAACATACCGGTTTTACCGTGGCATGGATAATCGCCAGTCTGA\n+TTGGGGCGTTAATGAACGGTATTTATTTGCAGGCGGTATTGAAAGGTTGGCGCAACAGCATGTTGTTTAC\n+CCTCGCGCTGTTGTTGCTGGATGGTGTGATGTGGGGACTCCTCAACTCTGCCGATAGCGCGCTGTTGTTG\n+GGAACCAGTGTGCTGGTGGTGGCGCTGGCCGGCATGATGTTTGTGACTCGTAATATCGACTGGTATGCGT\n+TTTCACTGCCGAAAATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAATTACGTATCTGGAAATAAGG\n+TTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGA\n+TCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTCGA\n+AATGTTTACGAATACGGCGGATCGTCACGTCTACAGTACGGTCGTGCGGTTTCAGCTCACGGCCGGTCAT\n+TTTCTTCAGCAGTTCAGCACGGGACTGAATTTTGCCTGGGTTTTCACAGAAGTGAAGCATGGCGCGGAAC\n+TCACTGCGCGGCAGCTTGTACTGCTCGCCATCAGGGCCGATCAAAGAACGGCTGTTGATGTCCAGTTCCC\n+AACCATTGAACTTGTAGCTTTCAACGCTACGACGTTCTTCGCTGACAGTACCCAGATTCATGGTACGGGA\n+CAGCAGGTTGCGTGCACGAATCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCG\n+ATTTCGAGGCCGAGAATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCT\n+GCTCGCGCAGTTCACGCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTT\n+GATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCC\n+GCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCT\n+GCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGC\n+ATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCAT\n+CAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGGCT\n+GTCATCCTAACCATTTTAACAGCAACATAACAGGCTAAGAGGGGCCGGACACCCAATAAAACTACGCTTC\n+GTTGACATATATCAAGTTCAATTGTAGCACGTTAACAGTTTGATGAAATCATCGTATCTAAATGCTAGCT\n+TTCGTCACATTATTTTAATAATCCAACTAGTTGCATCATACAACTAATAAACGTGGTGAATCCAATTGTC\n+GAGATTTATTTTTTATAAAATTATCCTAAGTAAACAGAAGGATATGTAGCATTTTTTAACAATTAAACCG\n+TTAGTACAGTCAGGAAATAGTTTAGCCTTTTTTAAGCTAAGTAAAGGGCTTTTTCTGCGACTTACGTTAA\n+GAATTTGTAAATTCGCACCGCGTAATAAGTTGACAGTGATCACCCTGTTCGCGGTCATTTGGTCAAGAAG\n+AGTGGCAATATGCGTATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGCGC\n+GGGCAATGAAAACGATGGGGTTTAGCGAACTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCAC\n+CCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACACTGGCTGAATCG\n+TTACACGATGTCGATTTCACTGTCGCCACCACTGCGCGCAGTCGGGCGAAATATCATTACTACGCTACGC\n+CAGTAGAACTGGTGCCGCTGTTAGAGGAAAAATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGTCG\n+CGAAGATTCCGGGCTGACTAACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGGCG\n+GATTATCCTTCGCTCAATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAATATTAATACAAC\n+AACCGACGAAAAGTGACACAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAGCCATGGCATT\n+GCTGACGACTCTGGCAGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTTTA\n+GAGCAACGAGACACGGCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAAAAAA\n+CGCCTTAGTAAGTATTTTTC\n' |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/reads_1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_1.fq Sun Jun 05 21:12:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@bacterial_std_err.000000000\n+ATTCCTGCGGTCACTAAGGGTTTAAAAGGCATTCCACCCTCCTAGAATTTTAACCACGGTGCAATGCCACAACGCCCGCCGTCAGATTGTAATAATCCACGCTCTCAAATCCGGCGTCCTGCATCACTGGCTTTTAAGGTATCCGGATCG\n++\n+IIHHHHIHHIIHGHIIHIHGIIHHHIGHIHGIHHIIGFIGHIGHGHHFHHIIGIHIGIIHHIIFFHIHIIIGIEEFCIIFHIDHIIIEGADIIIICIIDGAHIIHIDIFHIIIICGHIGIEIIFIDFIE@I@@FEIIIIIB<IE<IIEIG\n+@bacterial_std_err.000000001\n+CACTATCTGAATTGGTTATTTTTCGCGTCGTACAAGGCGTCGGGGAGCGATGATGATGCCAGTGGCGCGGCTGGCGTTATTGCGAGCCTATCCGCGTAGTGAGCTGCTGCCCGTTCTTAACTTTGTCACTATGCCGGGGCTGGTAGGTCC\n++\n+IIIIHHIIHIHHHHHHHGIIHIHHHIGGIIFHIHDIIIGIIGIIEIFFHIIGIHIHICGEDIIIFIHHCIIIDIIBDEGICIIDIIIIFIC@IIIIIIDICH>IDIIGIBHFIHHIIDHICIIIIHCDIHGHI=FDIIIIIFAIGGBI@I\n+@bacterial_std_err.000000002\n+TCATTAATGTATCAGCCTTTGTCATTTATCGACTTTTGTTCGAGTGGAGTCCGCCGTGTCACTTTCGCTTTGGCAGCAGAGTCTTGCCCGATTGCAGGATGAGTTACCAGCCACAGAATTCAGTATGTGGATACGCCCGTTGCAGGCGGA\n++\n+IIIIIHIHHIHHIIIHIHHIIIIIGHGHHIFHIHHFIHHIGDIIIGIHEIGHIIHGHFHIIIGIIIIGHI?IGIIAIII<IIEIIIDHEIIFIFGDCIIHIIEFFIIIIGCICHG=HIIFIHGFAIIIECEIDIIIIIGBIIIDIDHFEI\n+@bacterial_std_err.000000003\n+TGAAGCTGAAAGAGATCTCTTACATTCACGCGGAAGCCTATGCTGCAGGCGAGCTGAAACACGGGCCGTTGGCGCTGATTGACGCCGATATGCCGGTGATTGTGGTGGCGCCGAACAACGAACTGCTGGAGAAACTGAAATCCAACATCG\n++\n+IIIIIHIIIIIHIIIHHGHHGIHGHHIIIIIGGIIIIGIIHIGHHIGGIHIIIIEIFEEEIIIFGHDEIGIIIIGIFIHIIHCIIHFGICAIFIIGGIICIDFIIIIIFHDI@HIIGIIGAICIEIICHIIIEECI@IIIBIIIGAI>ID\n+@bacterial_std_err.000000004\n+TGGCCGATTTACAGAAATTCAGCCGCGTGATTGGCGACGATGTGTATCCGATATTGTCTTTGCAGTCTGTCTGGATAAACGGGCGGCAAAAGGCGGCGTTTCTCCGCTGCAGGTGGCGCAGGCCATCAACGATGCGAAGGCGCGCCTCGC\n++\n+HHIIHHHIHIHHIHGIIHHHHGGGIIIIHIIIIIIGIFIIIFGHGIIIHIIIEIIHIIIIFGFEIHIGFHCHIEEEIIFIEDIBIAIIEBGIIEIIGDECIDHIII>E@CIIHIHHIHHIIFFIHIEHCIFIIF@IFIH@IIIIBI@GHI\n+@bacterial_std_err.000000005\n+TTGTGCGCAAGAAAAGTTTCGCTCACACCGTAGGCCGGATAAGACGCGCAGCGGCGCCATCCGGCATAGCGGGTGATTATTCCCCGTCCTGAATCTCTTCGACCGGTGCCAGTTCACTAAACCAGCTATCCACCTTCTGACGTAACTTAT\n++\n+HIHIHHIIIHHHIIIIHHIHGIHGHIHHHIIIHIFIHHFIIGIGHHIIFGIIFEIIIEIEGGHIIIIBIGFIHIIIIDIFG>IIGHIIIDHIIHII@GHAIDBIIG@IEIIHIGIGFI>GIIIIHI9CDIIB5II=GBH=CIIIIIHIC?\n+@bacterial_std_err.000000006\n+CGCTGGCGGAGCTATGCTATAACACGCTGATCGAAGAAGGCGAAAAAGCCATGTTGGCCGCCGAACAGCACGTCGTCACGCCAGCGCTGGAACGCGTCATCGAAGCCAACACCTACCTGAGCGGGGTCGGTTTTGAAAGCGGCGGTCTGG\n++\n+HIHIHHHHIIIGHIIIIIHGIHIGGHIHHHGIIHGIIIGIGIIIIGIIGIIFHIIFIEEIDIDEGCIAIHHIIIEGGIIIIEEICIIIFBI@CCIIBGH@IIIDIGICFGII>CIIGIICIIGIIFI@IAI:FAG@EIIIBIEEIEFIII\n+@bacterial_std_err.000000007\n+CGTCGATGTTGTCGATACCACGGGAGCCGGTGATGCTTTTGTCGGCGGACTGTTGTTCACCCTTTCCCGCGCAAATTGCTGGGATCATGCCTGCTGGCGGAAGCCATCAGCAATGCCAATGCCTGCGGCGCTATGGCGGTGACGGCAAAA\n++\n+IIHHIHHIIIIHHHHHIHHHIIIHGHFIGGGHIIIHHIIGHIHIGIIIEHIIIIIDIICHIGIHIEIIEHEHIGGIIIIFHEDDIFIIFIH@DIHFDIDIIEECGIII@HFIGIEIIIEIBE@IIIBIIII?IH>CEIDAIIIEI=IGIH\n+@bacterial_std_err.000000008\n+GGAGCGTTATATGCCACTGGAAAAAGGAATTGCCGAATTGGTCGCTGGGTTTATCGCCGCGGGCCGCCCCTCTTCTCGCGAACAGAATATTGATGACCGGAGGGCGGGCTACATCGCCAGCACGACACTGGCAGGAGAAACAGAAACCCG\n++\n+IHIHIHHHIIIIIIHGIIHIHIHIHIIHIIIIGHIIGIIIGIIFIGGGEHCIIGDEGFDGIIIIDHIHIEFIEHIIIIGIEHFIFGIBGIEAIHE@FHI@FIIIDGI?FIIDDIF@GCICIEBIEHEIIIIII=IHIIEICIII<IDIDE\n+@bacterial_std_err.000000009\n+TTTTTAAACATCTGCTCTGGATCGATAATCAGCGCCCGATAACCCAGCATACCGGCACGGTTACTGTGNACTTTTAGCTCCAGCATCACATCCTGAGTACCGTCTTTGACTTCATCAAGAACGGAAACGATCGGTTTTGTACCGCTCATT\n++\n+HIHIIHIIHIIHHHIIIHIIGIGIIIFIGHIHHIGHGGIIIGIIIIIIEIGIIHIDIIGIIBIIIIFI!FDIIHEAGIHIGGIIAAEIDBIBDIEHGDHDIIEFIIBIIIIIIAI@9I@IIIIHIIICDBIIBIFHDCICCBFIIBIH>I\n+@bacterial_std_err.000000010\n+GCAGCGCTTTCGGGAAGCGACGCTCCATACGACCAATCATTTTCTGCGTGGCGTTATATTCAGAGACCAGTTTTTCTAACGCTTCGCCGGATAGCGCCGGCGCATGAGCGTTCGCGTGCAGAGTCGCACCGTCAAGCGCGATGGAAATCT\n++\n+HIHHIIHHHHHHIHHGHHHIHHHHGHIIFIHGHIIHIGIIGIFFIIIEGIFIEGIIIHGEIEIEEIFIGIHIIIGDIGDIEIIICIIIIGFEEIGIIICHIDGFIGIDFIIHEAFIIEIFIIDHI:IIGFIB=GIIIIIHI<IC6II@=I\n+@bacterial_std_err.000000011\n+AGAAAAAAGCCCATCCTGGGATGGGCTGAAAGTTTCCACGGCAACTCAAAAACTCCTGACGCCTTTCACGCTGCTGCTGCGTTGGCTGCCTTCGCTTACCCCAGTCACATCGCTATCTATGCTCCTGGGGATGTGCTCAGTTGCTGCCTT\n++\n+IIHIHIIIIHIIHHHHHIGIGGIGIIHIGIIGFHHGHIIIHIIIHIIFHHGGIGHHFIFIIDDIIEHIIEHIIGEDICDGGFGIIEI'..b'ACTGCCAATGCCAATTGCGCCGAAACGTACCGCGGAAAGATCGGGTTTCTGCGTCTGAAGGTCTTCATAGAAAGGGGTCAGGTTGTCCGGAATGTCTCCGGCACCGTGCGTTNAGCTGATTATCAGCCAGATCCCG\n++\n+IIHIHIIIHHIHHIHIHFIIIIIIIIHIIHIIIGIIIIDIIGIDIGIFFGIEIIGFGDHIFIIIIIIIGIHIGIIIIGIIIGIFCGIIIIIGFGIIIAII>IGIIIGBFIIIHIFDIIBIA:IIFE!HAHGIIIEDIIIIIIIIBHIBD<\n+@bacterial_std_err.000000989\n+CGNGTCACAGCATGAACACCACGCAGACGCAGAATATCGTGCGGCGCTTCCGGACCGTCGGAAATCACATCACCACGTTCTACACGTTCCCCTTCGAACACGTTGAGCTGACGCCATTTCGGAATCATCTCTTCGTACGGATCGCTACCA\n++\n+HI!HHHHIIHHIIHHIIHHIGHIHIIIIHHEIGIIGHGIIHIIGHGFDGIFIIIIHIEGHGDIIIIHIIIIIHH@IBBHIHGFEAEHG@IFIEEIIAIEIDDDII@EIIHIEII?DIC=GIICIIGHIB:IGIG<FII?IGDIIEHC@CI\n+@bacterial_std_err.000000990\n+CCAACCGGCGGACTCGGGTTCGCCATACCAGCTGCAACCTGCAGCTTGACGTAGGCTTGTACTTTCTTAGCCATTCTAAATTCCTCGAATTGGGTAGTAGCTTCAAAGAAGCTCCCCGTGATAAATATCGCTTTATGGGCATAAGGCCCA\n++\n+HHIIHHIIHHHHIIIHHIHIGGHHGHHGIIGIGIIFIFFIIIIHIHHGIHFIIFGIEIFFHCIIDFICIIIGFIIIDHIFDCI?IIIIIHICGHI>IEHCIEBECIIDIIIII@IFIIIIFEHI@CIIGCIIHFIIIIIIIGAGFGGII8\n+@bacterial_std_err.000000991\n+TCACTGGTTCGCCTCTCGGCGCGTACCGGCGAAGGCATCGACGTGTTGCGTAACCACCTCAAGCAAAGCATGGGGTTTGATACCAATATGGAAGGCGGCTTCCTGGCCCGTTGCCGTCACCTACAGGCGCTGGCGGAAGCCGCTGAACAC\n++\n+HHIHIHIIHHIHHHHHHIHHIIHIIGHGIIIIIIIIFGHHIEIFFIEIIHGHHHIHIIIIEIIIGIIGFEIIGHIIIDEIHIICGIIFIIEFHGIFIIEII@IIDIEHEHIBIDAFIAIIBEI>FIEDIHB?IIGEIII;?@AIDIIA9I\n+@bacterial_std_err.000000992\n+GATGGCGCGTTCGCTTATCCGGCCTACGCTATCTGTAGGCCCGGTAAGCGCAGCGCCACCGGGCATCAATAAAACTGCGCTTCTTCGGTGGAACCCGTTAACGCGTTAACGGATGACGCGCCGCCCTGAATAATGGTGGTGACTTTGTCG\n++\n+HIHHHIHIIHHIIHHHHIIIIIHIIIIIGIGIIIGGIFIIHIHHGEIFIIIIGEIIIIIIIICIGIFHHHFGDIEHIFEFEIHHGIFGIIGIH?FIGEIIIGIHI5HEIIHIGIDIIDIHICIEBHAIIIIAF=II@FII?IIII=II>>\n+@bacterial_std_err.000000993\n+TAAGGCGCCTTTTTTATGNCGTTGTCGCTGATTGCCGGATGGCAGCTTACGCCTTATCCGGCCCACCGGTATCCGCATTCTAAATCCTCTATGGATTTCGCGTCAGGGCAAGGCGGCAAGTAAGTGAATCCCCAGGAGCATAGGCCACTA\n++\n+IIHHHHHHHIGHIHGHIH!HGIHIHGIHHHGHGIGHIIHEHHIIHIIGHHIHHIEIIEGIHEIIFEIIFGIIIIIIIGHIHIGEIHIHFIEI7FIIIHBIGIIIHIHHFIIHDII:IIIAIIIIEHFI@HIIECIDDBEIII9EIBAIDF\n+@bacterial_std_err.000000994\n+AAAAACCCATGCTGTACGTCGGCGGTGGTGTTGGTATGGCGCAGGCAGTTCCGGCGCTGCGTAAATTTATCGCGGTAACGCAAATGCCAGTTACCTGCACGCTGAAAGGGCTGGGGGCTGTTGAAGCGGATTATCCGTACTATCTGGGCA\n++\n+IHIIHIIIIIIHGHIHHGIHHHHGHHGIFIHHHIFIFGGFIFHIGHIHGIFFIFFIIGIIGFIEIIHIDEIHIIIIDHIFHIDIIIIEIIEDIIEHFIIDID@IIDBHGII?CI<IGIIGI>EIIII@DIIBADCGAAEIIHHI?@IIHI\n+@bacterial_std_err.000000995\n+CGATCGCAGACATCCACCTTCTCAAAGGCGAAACGGTCGCTTTGCGCCACCGACGCCAGAGACATCAGGTTGCCCGCATAGGTGAGTTTATCCACCACCACCACCGCGTCTGCCGATTCATGGATGATATGCCGCACCACCGCAGATCCG\n++\n+IHHIHHHHHHHHHIIIIGGIIHGIIGHHGGIHHIIIGGIIIIIIHGFGGGIGHEIIFEGCIIIFIGHIIDIGFGIEFIFIHHFFGEBIIEBIDIFIGGF>DEIIEI>IIGIIIGI6EIIEIIIIIEIFDIIIBBIIH>IHHI>FICIIII\n+@bacterial_std_err.000000996\n+TTTTAACAAGTTTAACGTTTACGTAATGCTGAATGAGGGGACGCAATCGTTGCCGTACTAACAAATTGACGTGAAAAAAATTACCACACCACTGCGCCAGGTGTCGCATTTTGGTATAGGATAACGGCGAATTTTCCCTCCTTTCTCCGG\n++\n+HIHHHIHHHIIIIHHHIIHHIGIIIHIIIGIHIHIIHIFHGHHIIIIIIHGIHGHIGGIFIIHIFEFEIAGIIIEFICHHIHCIBIIIFFHIIFIIIIIIBIIIBGIDI@IHIIHEIIEIGIBGIIGHIFCHIIDFIHA@IIIICIDICI\n+@bacterial_std_err.000000997\n+GCTGCACGTGAGTGAAGCGGTGCCGGCGGCCTTTGGCCTGTTCGCGTGTTGTCCGAATTCTGCCGTAGATGCTATTATCTCCGGCGTTAATATCGGCAATGATCTGATACNGTCGCCACCATGGTCGGGGCGATTTCCGGCGCATTCCAT\n++\n+IIHIHIHHIIIIIGHHIIIHFHHIIGHIIFGGHGIFGIIHHGIDDHHIDIIGGIFGIIGEHIIIIIFIICAGGGFICDIDGIICDGA@IIHGHHEIIIDIIIGIEFFIGI!GEHDIIID=IIFGIIEDDIFIIIGH=G?I@IDGHIIIGI\n+@bacterial_std_err.000000998\n+CGTATGGCGCGATGGTACCCGCGATTACCAAGAACCCGGATGAACGCGCCTCGCTTGCCGCCTGGCGTCAGGGCGGCGCCACTCTCGGCCTGCTGCTGTGTACCGTTGGCTTTGTGCCGGTCATGAACCTGATCGAAGGCAATGGCCAAC\n++\n+IHHIHIIIIIGHHIHHHIHHIIIGGFGHGGGIIGIIHGIHIHGFIGHIHHGGGIFIFIIIGIHFIHDIIIHEEIFIIIDIGHGHCBECIFIDIHEIIBIIA?DIHIG<EEFHICIBIIGEFF<IGIIIIH@I?IIIFC?HCFIF6GIIFI\n+@bacterial_std_err.000000999\n+GAATCTGTAAATTTCAATGATATTATTTATAGGTTATTCTAATGAAAAAGGATTTGTTATCATCAATTATTATCGCTATGCTGATGACTGCCGGGCTAAGCTCTTGTGATGAAAAAAAAGCTGGCGAACAACCTGTAGCTCAGAGTGCGG\n++\n+HHHIIIHIHIHHHHIHIIGHGIHIIHIIGIIIIIFGGGIFHHGFDIIIFIGFCFIHIIGHHIIIFHEIIHHIIIIIIFIIIHGAIIEIGHIIIIII>IGHGHHIIIHIIGIII@E@F@BHEIC9IBIIICEBDIFIAIIIIIIIIC@HID\n' |
| b |
| diff -r 000000000000 -r 0801bffdfcc8 test-data/reads_2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_2.fq Sun Jun 05 21:12:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@bacterial_std_err.000000000\n+AATTTTCACGTATGGTCGGGGAAACTGGCAAAGTTATCCTGGCGGATATTAATGATTCCATGCTCAAAATGGGGCGTGAGAAGCTGCGTAATATCGGCGTGATCGGCAACGTAGAGTATGTGCAGGCGAATGCCGAAGCTCTGCCTTTCC\n++\n+HHHHHHIHIIIGIIHIGHHIGHHGIHGGGIIIIGIIEFIIIGIDIGIGGGIGIIDIHHIIFGIFIFIHIIIIHDDGFIIIIIIEIHHIEIICIIDBIIIIBI@IHIHG@DGDIFEI@IHEGIIAEFIII?DICIIIHBI=IIDIGIFIIG\n+@bacterial_std_err.000000001\n+AGAGCCGGGTAGCCAAAACCAACTGTAGCATTAACGGCATCAAAAAAGGTACGCANCCTGTCCCCAGACGCGTGGCGAGGTTGCCGGCAATACCGACGGAAAATGTGCGTGTCTTAAACAGCGATAGTGATATTAACGGTGTCGGATGAC\n++\n+IIHHHHIHHHIIHHIHIGHIHIIIHIIHIHHHIIGIHIIIGGEIIIIEFIIIGGI!IIGIGIIHIIDDIIBIIIIGIHIIIHEGIFIIIGIFIGGCIGAIFIIIHGDGIIIIFIIIICFCG?IIIIIGIDIGCCII;FIII?IIIEIIID\n+@bacterial_std_err.000000002\n+GGTCGGCTGGCTCTGGTACGTTATCCCAGCCCGAACGGGCCGCAGGCGCTACGCGCTGCGGCTGCGCCGTTGTTGTCTGCGCAGGCGCGACAACGTTATGCACAGGCGTTTTTAGCGTTTGCGTAACGGGCTTTGTTCCCACTTCAAAAA\n++\n+IHIIHHHIHIHFHHHHIHFIHHIGHIHHIFIGHIIIIIHFIGIIIEIFHIIDIGGIGHHIIHGDIIIGHIIEIEFIIHDEHACIEFEIICHIDIIIHIIHIDHFIIDHIFFIIIHIGHGIFBHHFIIFIIIII;IIHIIHIGIIBIGII;\n+@bacterial_std_err.000000003\n+ACCTCTTAGTCGCTCTTCAGCCACCATNGATAGGAAAGAACAGCGCCTGTCACAGCGCACAAAAAAAGGCCGGCTGTCGACGGCCTTCTGCCTGGTACTACATTTGTACTTACTCTACGGTAACCGATTTCGCCAGGTTACGCGGCTGGT\n++\n+IIHIHHHHHHIIHHHHGGIGIIIIHGH!HEHIIHGHIEGIHHGIEHIIEIGGIIGGHHIFEIIIIIGIIHDGDBHIIIIIFII>IFC@GIIEGIDIFBIEACBHDFIFIFD>H@CIIIHIIIIICIIIH?I@DEGGHIIIIFEIDIHICI\n+@bacterial_std_err.000000004\n+GTAGCATAGCAATGAACGATTATCCCTACAACCTTGCTGATTAATAATACATCACAGAACGGAGCGGTTTCTCGTTTAACCCTTGAAGACACCGCCCGTTCAGAGGGTATCTCTCGGACCCGAAATAACTAAAGCCACGTGAACTTTTGC\n++\n+IHHIIHHHHHIIHHIIHIIIIHIHGIIIHHIIFIGGHFIHIIIIHFIIIIIEGGIIFIIHIFIIIIGHIHIIIGHIDIIHHIGGIIIIIIIGIHEI@I?IIIII@DIIIHGBIDICCIAGIFIIDAGIIBIG>II?HIGBIIDH?=HB=F\n+@bacterial_std_err.000000005\n+CGGGCTATGGCTACGCGGAAGTCCCGGAAGAGATGAAACGCAAGTGGCAACGCGCGCTGGGGGAATATCTGGAGAAACGTCAAAGCCTACAGGGCTTAGTCGGTTTAATGGATATCCGCCATCCGTTGAAAGACCTCGACCAACAGATGA\n++\n+HHHHHIHHHHIHIIIIGIIIHIHIGIIGIGIIIIGHGIIIIGIIIHIEHHDDIGFIEHIIIIEIGIHGBGII@EIIIHGFEG@AIIEIIIBICDIFIIIEED9FIH?IIIEIIIIIHIIA=BIA=AIIIBGCAACII>AII@EIIIIICB\n+@bacterial_std_err.000000006\n+TGACTATCGTCAGGAGTATTGCTCAGACCTTATTCCCATTCCTGCAAGAAGCGTTGACCGTACTGGTCGGCGACCAGCAGCGCGGCGTACACTTCATCCGGCGTTGCGCCGCCAGGCATGTTATGAATAGTTTCACCTTCTGCGCAGGAG\n++\n+HHIIHIIHHHIIIGIHIIIIGIHHHHHGIGGHGIIIIGIHGHFIGGIIHHIIIIIDFIIIEBFIIIIHIIIIIDIGEIHIAHFGGEIIIIHGFICHGIF?>CIFIBGCCIEEIIICAIIIIGIEEI@EEI?F=DGHDEGIIGDIIIIIBI\n+@bacterial_std_err.000000007\n+TGCTGGAAAGCCTCGCGCATCGCCTCGTCGCTGACCTGGCGTTGATGGCGCAGCAGCGCATCCATGATGTACTTCGCCTGAATAAAATCATCCGTGCACATCCCCGCTTCGTTGCAGCGGCCAAACGTGTCAGCTGGCGGTTTTTGAAAG\n++\n+HHIIHHHIIHHIHHIIIIHIIHHHHIIEHIIFFGIFIIIIGIFIIHIIIEIIHIIIHGIHIEHFGIIFIDGIIFFIHEDIIIGBFEIIIHDFGIEAEIEIIIIIIIGIBCGIGIDIICIGIDI>IGCHGIDIDIEIII<IIDII;BIIDI\n+@bacterial_std_err.000000008\n+TGAAAGCAGCGTGTCACGCGTGATAATGTAATCCAGCCCATTACAGGTGTAGCTCGCAAACCTGGCGGTTGCGTCCAGCATGGGGTAGATCAGAATCAGCTGTGCAGGTTGCCATTGACGGGCGGCTTTCAGGCGTAGCGCGGTGACCAG\n++\n+HIHIIHHIIIIHIIHIGHIIHGIHHIIIIIHIHIIIIIHFIGIIIGEIGHIIIFGHHIIIHEHGIAIGCIIDHHFGFIIEDIIIIHEIFIIIIIIGIHIIIFGH>IIDIFDIGEIIIIECHI=IGIIFDIIDIHCIICDIIIEIIIECIA\n+@bacterial_std_err.000000009\n+GCGACGGTGGATTTGACTGGACATGGACACAACATACCGGTTGGTTAGTGCCATCCAAAAGCACCGGAGGTAAAACCGTCGTGACCGCCTTTGATAACGGCGATGCGCGCGGCATGGAACAACCGGCCATGCCATCAATGAAATATTCCC\n++\n+HIIHIHHHHHIHHIIIHIHIHHIHHGHHHIIGGIIHGGIIIIIHGEEIIFIGGFEIEIIIIIDIHIIFCHIIFFIIIIFHIIDIFIIIHDEDGII?GIIIIIFEIHIAFCIIFHIFIIBIIIGHBDI=EIIFIIIFCFFII@IIAIG@II\n+@bacterial_std_err.000000010\n+AGGGGCGTAACCGCAAGAACCAGGCGATTCTGCCGCTGAAAGGTAAAATCCTTAACGTCGAGAAAGCGCGCTTCGACAAGATGCTTTCCTCCCAGGAAGTGGCGACGCTGATCACCGCGCTGGGCTGCGGTATCGGTCGCGACGAGTACA\n++\n+HIIIHIIIHIIHHIIIHIIIIHIGIIIHIGIHHGIHIIGHIHEGGIIIHFIEGIGIHGIGIIFIGIIIIIIBIGHFHCIDII@IIIEDIHIDDFIII@>IDFIHGIIHIICIIBFIIIIII>DIDIIBGIAFDIGDIICIIIIIIFIAHG\n+@bacterial_std_err.000000011\n+GCTGGCCTACTCCGCCCGTAACCGTTCCGCCTCCATCCGTATTCCGGTGGTGGCGTCTCCGAAAGCGCGCCGTATCGAAGTTCGCTTCCCGGACCCGGCGGCTAACCCGTATCTGTGCTTTGCCGCCCTGCTGATGGCCGGTCTGGGCGG\n++\n+HIIHHHHIIHGHIIHHIIIGGHIHHIIICIHGHIIHIGIHFIGGGDIGIIIIIIIHIEFDGHFHFIIIIBIEIIDIIHFIIEDHIGB'..b'CAGAACCCGATCATGCGCACCATCAAGCCATGATCGGCTTTTTTAATCACACATTTTTCCACAGGTAGATCCCAGCTCGTTCACAGAGTACAATGCAGCCTCTTTACCTGAGCGAGCGATCGATGGCAGACATTAC\n++\n+HHHHHHIHIHIIIIGHHHHIHHIGIIHGIIIHGGHIHHIGHGHIHIEIIIIFFEFFIGFIIIGGIEIGIEGIIIGIIGIIFDBIIEIFIIAIIFIIG>IB@IEHHIIIIIIIEEBIAIIIFHH>IIIGGIIIIBIIBGIDIGIIFIDAFG\n+@bacterial_std_err.000000989\n+AACTGACCGGTTTGTCTTCGCTGGTGGTTCTGGATTCGGCTGAACGTACTACCGGTGGTAAAGATCTGCGTCCGGCGCTGAAAATCGTTGATGCTCAGGGTAATGACGTTCTGATCCNGGGTACCGATATGCCTGCGCAGTACTTCCTGC\n++\n+IIIHIHIIHIHHGHIGHHIIFHGIIIGGIIIHGHIHIIHFIIFGGFIIIIIIFIIIHFHEIIIGFGIIFIIIHIDDHDI>BGFFDIEGIFIIIGIDFIIEIIIIEIGIF?GIIEIII!IGCIIECIFBIAGI@IIIIIGIIEIBIGIIDI\n+@bacterial_std_err.000000990\n+NAAGAAGTCGATGCGATCATGAACCGCCTGCAGCAGGTTGGCGATAAGCCGCGGCCGAAAACTCTGTTTGAACCGGGTGAAATGGTTCGTGTTAACGACGGTCCGTTCGCAGACTTTAACGGCGTTGTCGAAGAAGTCGATTATGAGAAG\n++\n+!HIHHHHHHHGHHHHIIGIHHIHHIIHIHIGHHDGFIHGHHGHGIGFGGFIGIGIHIIIDIGIHFIFIIGFFIHIGDDIIIIFHEIFEGGGIIIDIIIGIHIICIIEHI;DICIFIFCIGIHEIGIGIGH>CDAIB?IFIEEBBC=GH=I\n+@bacterial_std_err.000000991\n+AGGACACAAAAATCGCGGATGTAACCCGCACGACTATGGACGAGTATGGAAAGTAAAAACCCGCGTTAACAGGCAGTTAATGCGGGTTAGTGAACGTTCACTGACGAGGGTGGACTAAAACTTACTTACCGATACAGAAGCTGGAGAAAA\n++\n+IIHIHHIHIHIHHHHIIHHIHBHHHHIHIHIHIIIIEHIIIGGIIFIIIIIIEGIIIEIFCIEGGIHGHDIGHIEHIIIAIIHIICGIIIIIIFIIGGIDDECIIEIIC>IFIG?IIIFII?II>DIGAEIIIIIIIH@HAD?DIDIIDE\n+@bacterial_std_err.000000992\n+TGCCGATGCTATCCACGCGAAGTATCCGGGCAAACTGCTGGCCTATAACTGTTCACCATCCTTCAACTGGCAGCAAGAATCTGGACGACAAGACCATTGCCAGCTTCCAGCAGCAGTTGTCGGACATGGGTTACAAATACCAGTTTAATA\n++\n+HIHIIIHHHIIIHIHHIHHHIHHIGIGIHHIHHIIGFIHDHHHIIHIGIEFECIEGIFEIEEIFHIIHHCIGGGIIDCHIIIICIDIEIIAIDEIIIIIIIIHIIFIGFDFGI@IIDHFIIBIFEIFBCIIFI@E;IAIICIIGI;IADG\n+@bacterial_std_err.000000993\n+TGTTTGAGAAACTNGATGCAAAAGTACAGCAGGCGATTGACACCATCACCCTGTTACAGATGGAAATTGAAGAGCTGAAAGAAAAGAACAACAGCCTGACGCAGGAAGTGCAGTCTGCACAGCATCAGCGTGCAGAACTCGAGCGTGAAA\n++\n+HHIHHIHHIIHIH!IGIFHHGIGHGIIHIHIIIIIIIIIGEIIHIFFIGGIIIIIEHHHGIIDIG@IIIIDCIIHFFIHIIIIBCIIFEIFDDIGGHEGHIII=IFGDICCIIIG@IGFHIFIIIEIIFBEI8IIHIIIIIIIGI;IIDI\n+@bacterial_std_err.000000994\n+CGCGCAGCTCTGCACAGGACTGACGCCATGCGTCGTTCTTCAGCGGTTGCTGTAATGCCGGCAACAGCGAATTTAAATCGCCCTGCAACGCGACGTGTGCCTGACGCAGTTTGTTCATTTCCGCCGGGTCGATATCCATATGGATTACGC\n++\n+HIHHHIHHHHHIIIGIIHGIIHIIHHIIIHHIFGGHGHIGIGIHFFGGIIIFIIIFIEIIEFHIEIIIEFGIIIHIGHIEBIIGIIIGGIBIFIIE?DIIEI8IIHIIGEEIAIIAICI>?FIIIBIFGIIEIIIIIIICCGBIIIIIII\n+@bacterial_std_err.000000995\n+CGCAAAGTAATCGCCCGCTGGCACAGCGGCGAAACCCTGGTCGTTCGAACCGAATATCCGTCAGTTGCCGAAAAAATTGGACGGACTTTGTACGCTGGCGAAACTGGACGCGGCGCTGCCCGCCGCCGATGTGCTGGTGATGCTGGTCGA\n++\n+HHHHHHHHIIHHHIHGIHGHHHIIGGIIHIHHIIHGIIIHHIIEIFIFIGIGDIIBHIIGIIFIIIICHBFDEIIEHIFIIHGIHFIIHEICCHEIGIAIAFIHH@IHIDAGII?I?E9E>CCIFII?GIEI@DGIHIFFFIIACHFGGI\n+@bacterial_std_err.000000996\n+CACGGCAGTCCCATTGCCTGCACAACCACGAAGGCAAAGAACGCATTCAGCCCCATCGCGGGCGCCAGCGCAACCGGCAAGTTAGCGAACAGGCCCATCAGAATACTGCCAAAGGCCGCAATCAGACAGGTGGTCACAAAGACGGCGCTG\n++\n+IIHIHHHHHIHHIIHIIHIIGHIHIIIIHGIFHGIFIIHIFIGIIDFIHIHIEFGIIIIDDHHIBIDHIDI@GIEIIIGFIFIIGF?HDIHIII;EEEHEICEIIHIIIIGIGIIIIF>FIBGGIIIIEIII5G?I>;CEIEIBIFIE??\n+@bacterial_std_err.000000997\n+TAGCTCACGCCTTCCGGCACCGAGCACACCACCGAACCACTTCCGCGCTGGGAGGAAATAATGCCCGCATTGATTAATTCGCTCCAGGCCTGTTTAACCACACATCAGCGAGACGTTGTAGGATCTGGCAATCTCTTTTTGCGTCGGTAG\n++\n+IHHIIIIHHIHHHIHIHHIIFIIIIIHHIGHFGHIIIIHGFHGIFIGIGHIHGHGHGHIIIIIIIGEIIIFGIGIIIIIIIIEFGIIIIHCIGIIHHBIHDA7IIGIIBG@IHIIIIC?IGGGIDCEDIIHHFCDBEIAE;II@FB?>ID\n+@bacterial_std_err.000000998\n+TATTAACAGCCCGCCGATATAGACTTTCTTCTTGCCAAAACGCCTTACAGCGCCGGAGCATCAAAAAAACGCCGATAAAAATACAGCCCATGCTAAAGAAGCCCATCCAGGAGAGGAGGATCGGGTCNTTAAGAACGTACTGGGTGTAAT\n++\n+IHIHHHIIIHIIHHHIIIGHIGGIIIHGIIHGHIHIHIIIFGHIHIIIDGHHHFIIEIHIGIIEEIHCIIEDEIGCEGGIIIBIDFIIIIIGIFIEFDIHIIABIFI@FHIIIIIAI=IGGIGIIDH!IDIIIGCDGIGICDIIIBFIFI\n+@bacterial_std_err.000000999\n+ACTCATCGAACTGTTTTATAAACGTTTTATGGAACGCTTTAGCGCCAGCAAAGGCATCATCCTTGAAGTTATCTTGATCATAGTATTTATTCATACTATTGATTGTTTCAGCTAGTGGCCCAGCCGCATTAATAAATGCCAGAGCAGCAC\n++\n+HHIHHHHIIHIHIHIGGHIHIHHHHGFHIIGIIIIFIHGHIIGIIGIGIHIHFIEGGHDGDFIIFEFICIFHF@IHDIIFCIDI@FIIAIIDFIIIIEIEIEFEIHIIIIGDI?IIGBII=IDIIIGICF=H?GIIIFAIIIIFHCF=I?\n' |
| b |
| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.aligned.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.aligned.fa Sun Jun 05 21:12:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,91642 @@\n+>gi|15829254|ref|NC_002695.1|\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+-----------------------------------------'..b'----------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+--------------------------------------------------\n' |
| b |
| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.consensus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.consensus.fa Sun Jun 05 21:12:39 2016 -0400 |
| b |
| b'@@ -0,0 +1,91642 @@\n+>gi|15829254|ref|NC_002695.1| Escherichia coli O157:H7 str. Sakai, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTC\n+TGACAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG\n+TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC\n+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCACCACCATCACC\n+ATTACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCC\n+CGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAG\n+TGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATA\n+TTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAA\n+TCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCA\n+ATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGC\n+CGGGATTCCCGCTGGCGCAATTGAAAACTTTCGTCGACCAGGAATTTGCCCAAATAAAAC\n+ATGTCCTGCATGGCATTAGTTTGTTAGGGCAGTGCCCGGATAGCATTAACGCTGCGCTGA\n+TTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTC\n+ACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAAT\n+CTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATC\n+ACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTACTTG\n+GACGCAACGGTTCCGACTACTCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTT\n+GCGAGATTTGGACGGACGTTGACGGGGTATATACCTGCGACCCGCGTCAGGTGCCCGATG\n+CGAGGTTGTTGAAATCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTA\n+AAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTA\n+AAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGTCGTGATGAAGACG\n+AATTACCGGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCC\n+CGGGGATGAAAGGAATGGTCGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGCCC\n+GTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTC\n+CGCAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGA\n+AAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGGCTGGCCATTATCTCGGTGGTAG\n+GTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCGCTGGCCCGCG\n+CCAATATCAACATTGTCGCTATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGG\n+TAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCG\n+ATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGC\n+AACTGAAGCGTCAGCAAAGCTGGTTGAAGAATAAACATATCGACTTACGTGTCTGCGGTG\n+TTGCTAACTCGAAGGCTCTGCTCACCAATGTGCATGGCCTAAATCTGGAAAACTGGCAGG\n+AAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAG\n+AATATCATCTGCTGAACCCGGTCATTGTTGACTGCACCTCCAGCCAGGCAGTGGCGGATC\n+AATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACA\n+CCTCGTCGATGGATTACTACCATCTGTTGCGTCATGCGGCTGAAAAATCGCGGCGTAAAT\n+TCCTCTATGACACCAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGC\n+TCAATGCTGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCAGGTTCGCTTTCTTATA\n+TCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACTACGCTGGCGCGGGAAA\n+TGGGTTATACCGAACCGGATCCGCGAGATGATCTTTCTGGTATGGATGTAGCGCGTAAAC\n+TATTAATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAAC\n+CTGTGCTGCCCGCAGAGTTTAACGCTGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGT\n+CACAGCTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTT\n+TGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGG\n+ATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTTTATAGCC\n+ACTATTATCAGCCGCTGCCGTTGGTGCTGCGCGGATATGGTGCGGGCAATGACGTTACCG\n+CTGCCGGTGTCTTTGCCGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATG\n+GTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGG\n+GCGGCGGTGACACCCGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGTCGGCA\n+GAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGG\n+GAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTGGGCAAGCAAATTCCA\n+GTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGT\n+TCGGTGGTCGCGGCTCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACC\n+CGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGAC\n+AACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATC\n+AGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAA\n+GTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATT\n+GCGCACGGGCGACACTTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTT\n+GCCGCGAAGCTGATGAAAGATGTTATCGCAGAACCCTACCGTGAACGGTTACTGCCTGGC\n+TTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGC\n+TCCGGCCCGACCTTGTTTGCTCTGTGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGAC\n+TGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGAT\n+ACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTTAA'..b'CTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACT\n+GGATAACGCCATCGATTTTACCCCCAAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGA\n+TCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCT\n+GTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGG\n+TCTGGGGTTGGCGTTTGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCG\n+CAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGGCTTCACCGTCACTTCACATAGCT\n+TCAAATTCTTCCCACATAGCCTTCGTATCCTGCTGCCATTGCAAAGGAGAAGACTATGTT\n+GAAATCCCCCCTGTTCTGGAAAATGACCACCCTGTTTGGTGCAGTATTGCTGTTGTTGAT\n+TCCGATAATGCTGATTCGGCAGGTGATTGTCGAACGTGCCGATTACCGTAGCGATGTGGA\n+AGATGCGATTCGCCAAAGTACCAGCGGGCCGCAAAAACTCGTTGGGCCTCTTATCGCTAT\n+TCCTGTGACCGAGCTTTATACGGTGCAGGAAGAGGATAAAACCGTGGAGCGGAAACGAAG\n+TTTTATCCATTTTTGGTTACCTGAGTCATTGATGGTTGATGGCAATCAGAACGTGGAAGA\n+ACGCAAGATAGGGATTTATACCGGTCAGGTCTGGCACAGTGATTTAACGCTAAAAGCCGA\n+TTTCGATGTTTCGCGTCTTAGCGAACTCGACGCGCCAAATATCACCTTTGGCAAGCCATT\n+TATTGTGATTAGCGTCGGGGATGCGCGTGGTATTGGTGTGGTGAAAGCGCCTGAAGTTAA\n+CGGAACGGCGCTGACTATTGAACCCGGCATCGGGTTAGAGCAAGGCGGGCAGGGCGTGCA\n+TATCCCTTTACCCGAAGGGGACTGGCGGAAGCAGAACCTGAAGCTGAATATGGCACTGAA\n+TTTAAGCGGTACCGGCGATCTTTCTGTGGTGCCTGCGGGGCGTAATAGCGAAATGACCTT\n+AACCAGCAACTGGCCGCATCCCAGTTTTTTAGGTGATTTTCTACCAGCCAAACGGGAAGT\n+TAGTGAGTCAGGTTTTCAGGCGCAATGGCAAAGCAGCTGGTTTGCTAATAATCTCGGTGA\n+GCGTTTTGCTTCAGGCAATGATACCGGCTGGGAAAACTTCCCCGCGTTTAGCGTCGCAGT\n+GACGACGCCCGCCGATCAATACCAATTAACTGACCGGGCGACTAAGTATGCCATTCTGCT\n+GATTGCGCTGACTTTTATGGCGTTCTTTGTTTTTGAAACGCTCACCGCGCAACGTTTACA\n+CCCAATGCAATATTTGCTGGTGGGGCTTTCATTGGTGATGTTTTATTTGCTCTTGCTGGC\n+GCTTTCTGAACATACCGGTTTTACCGTGGCATGGATAATCGCCAGTCTGATTGGGGCGTT\n+AATGAACGGTATTTATTTGCAGGCGGTATTGAAAGGTTGGCGCAACAGCATGTTGTTTAC\n+CCTCGCGCTGTTGTTGCTGGATGGTGTGATGTGGGGACTCCTCAACTCTGCCGATAGCGC\n+GCTGTTGTTGGGAACCAGTGTGCTGGTGGTGGCGCTGGCCGGCATGATGTTTGTGACTCG\n+TAATATCGACTGGTATGCGTTTTCACTGCCGAAAATGAAAGCCAGTAAAGAAGTTACAAC\n+GGACGATGAATTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGC\n+CGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACC\n+TTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTCGAAATGTTTACG\n+AATACGGCGGATCGTCACGTCTACAGTACGGTCGTGCGGTTTCAGCTCACGGCCGGTCAT\n+TTTCTTCAGCAGTTCAGCACGGGACTGAATTTTGCCTGGGTTTTCACAGAAGTGAAGCAT\n+GGCGCGGAACTCACTGCGCGGCAGCTTGTACTGCTCGCCATCAGGGCCGATCAAAGAACG\n+GCTGTTGATGTCCAGTTCCCAACCATTGAACTTGTAGCTTTCAACGCTACGACGTTCTTC\n+GCTGACAGTACCCAGATTCATGGTACGGGACAGCAGGTTGCGTGCACGAATCGTCAGTTC\n+ACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGAATTTT\n+ATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAG\n+TTCACGCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTT\n+GATGTCATATTCAGAGAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATC\n+ATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAC\n+GATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAATTGCCAACTAAATCGAAACAGG\n+AAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAACATGATCGGCGTAACA\n+TGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTA\n+GCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGGCTGTCATCCTAA\n+CCATTTTAACAGCAACATAACAGGCTAAGAGGGGCCGGACACCCAATAAAACTACGCTTC\n+GTTGACATATATCAAGTTCAATTGTAGCACGTTAACAGTTTGATGAAATCATCGTATCTA\n+AATGCTAGCTTTCGTCACATTATTTTAATAATCCAACTAGTTGCATCATACAACTAATAA\n+ACGTGGTGAATCCAATTGTCGAGATTTATTTTTTATAAAATTATCCTAAGTAAACAGAAG\n+GATATGTAGCATTTTTTAACAATTAAACCGTTAGTACAGTCAGGAAATAGTTTAGCCTTT\n+TTTAAGCTAAGTAAAGGGCTTTTTCTGCGACTTACGTTAAGAATTTGTAAATTCGCACCG\n+CGTAATAAGTTGACAGTGATCACCCTGTTCGCGGTCATTTGGTCAAGAAGAGTGGCAATA\n+TGCGTATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGCGC\n+GGGCAATGAAAACGATGGGGTTTAGCGAACTGCGGATTGTCGATAGTCAGGCACACCTGG\n+AGCCAGCCACCCGCTGGGTCGCACATGGATCTGGTGATATTATTGATAATATTAAAGTTT\n+TCCCGACACTGGCTGAATCGTTACACGATGTCGATTTCACTGTCGCCACCACTGCGCGCA\n+GTCGGGCGAAATATCATTACTACGCTACGCCAGTAGAACTGGTGCCGCTGTTAGAGGAAA\n+AATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGTCGCGAAGATTCCGGGCTGACTA\n+ACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGGCGGATTATCCTT\n+CGCTCAATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAATATTAATACAAC\n+AACCGACGAAAAGTGACACAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAG\n+CCATGGCATTGCTGACGACTCTGGCAGTGGCAGATGACATAAAACTGGTCGACTGGTTAC\n+AACAACGCCTGGGGCTTTTAGAGCAACGAGACACGGCAATGTTGCACCGTTTGCTGCATG\n+ATATTGAAAAAAATATCACCAAATAAAAAACGCCTTAGTAAGTATTTTTC\n' |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.csv Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,1 @@ +CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,LOCUS_TAG,GENE,PRODUCT |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.depth.gz |
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| Binary file test-data/test/snps.depth.gz has changed |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.depth.gz.tbi |
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| Binary file test-data/test/snps.depth.gz.tbi has changed |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.gff Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,1 @@ +##gff-version 3 |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.html Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,16 @@ +<TABLE ID='snps' BORDER=1> +<TR> +<TH>CHROM +<TH>POS +<TH>TYPE +<TH>REF +<TH>ALT +<TH>EVIDENCE +<TH>FTYPE +<TH>STRAND +<TH>NT_POS +<TH>AA_POS +<TH>LOCUS_TAG +<TH>GENE +<TH>PRODUCT +</TABLE> |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.log Sun Jun 05 21:12:39 2016 -0400 |
| [ |
| @@ -0,0 +1,66 @@ + +### samtools faidx reference/ref.fa + + +### bwa index reference/ref.fa + +[bwa_index] Pack FASTA... 0.04 sec +[bwa_index] Construct BWT for the packed sequence... +[bwa_index] 2.34 seconds elapse. +[bwa_index] Update BWT... 0.04 sec +[bwa_index] Pack forward-only FASTA... 0.03 sec +[bwa_index] Construct SA from BWT and Occ... 0.61 sec +[main] Version: 0.7.12-r1039 +[main] CMD: bwa index reference/ref.fa +[main] Real time: 3.079 sec; CPU: 3.060 sec + +### (bwa mem -v 2 -M -R '@RG ID:snps SM:snps' -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq | samtools view -@ 1 -q 60 -F 3844 -S -b -u -T ref.fa - | samtools sort -@ 1 - snps) + +[samfaipath] fail to read file ref.fa. +[M::mem_pestat] skip orientation FF as there are not enough pairs +[M::mem_pestat] analyzing insert size distribution for orientation FR... +[M::mem_pestat] (25, 50, 75) percentile: (429, 488, 536) +[M::mem_pestat] low and high boundaries for computing mean and std.dev: (215, 750) +[M::mem_pestat] mean and std.dev: (479.53, 81.93) +[M::mem_pestat] low and high boundaries for proper pairs: (108, 857) +[M::mem_pestat] skip orientation RF as there are not enough pairs +[M::mem_pestat] skip orientation RR as there are not enough pairs +[main] Version: 0.7.12-r1039 +[main] CMD: bwa mem -v 2 -M -R @RG ID:snps SM:snps -t 1 reference/ref.fa /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq +[main] Real time: 0.268 sec; CPU: 0.262 sec + +### samtools index snps.bam + + +### samtools depth -q 20 snps.bam | bgzip > snps.depth.gz + + +### tabix -s 1 -b 2 -e 2 snps.depth.gz + + +### fasta_generate_regions.py reference/ref.fa.fai 1397543 > reference/ref.txt + + +### freebayes-parallel reference/ref.txt 1 -p 1 -q 20 -m 60 -F 0.9 -C 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf + +WARNING(freebayes): Could not find any mapped reads in target region gi|15829254|ref|NC_002695.1|:1397543..2795086 + +### vcffilter -f 'DP > 9' -f 'QUAL > 10' snps.raw.vcf > snps.vcf + + +### bgzip -c snps.vcf > snps.vcf.gz + + +### tabix -p vcf snps.vcf.gz + + +### /usr/local/Cellar/snippy/2.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab + +Loading reference: reference/ref.fa +Loaded 1 sequences. +Loading features: reference/ref.gff +Parsing variants: snps.vcf +Converted 0 SNPs to TAB format. + +### vcf-consensus snps.vcf.gz < reference/ref.fa > snps.consensus.fa + |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.tab Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,1 @@ +CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS LOCUS_TAG GENE PRODUCT |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.txt Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,6 @@ +DateTime 2015-07-08T02:17:02 +ReadFiles /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_1.fq /Users/Simon/code/galaxy-wrappers/snippy/test-data/reads_2.fq +Reference /Users/Simon/code/galaxy-wrappers/snippy/test-data/Ecoli.fna +ReferenceSize 5590174 +Software snippy 2.6 +VariantTotal 0 |
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| diff -r 000000000000 -r 0801bffdfcc8 test-data/test/snps.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/snps.vcf Sun Jun 05 21:12:39 2016 -0400 |
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| @@ -0,0 +1,57 @@ +##fileformat=VCFv4.1 +##fileDate=20150708 +##source=freeBayes v0.9.21-7-g7dd41db-dirty +##reference=reference/ref.fa +##phasing=none +##commandline="freebayes -p 1 -q 20 -m 60 -F 0.9 -C 10 -V -f reference/ref.fa snps.bam --region gi|15829254|ref|NC_002695.1|:0-1397543" +##filter="DP > 9 QUAL > 10" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> +##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> +##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> +##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> +##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> +##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> +##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> +##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> +##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> +##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> +##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> +##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> +##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> +##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> +##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> +##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> +##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> +##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> +##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> +##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> +##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> +##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> +##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> +##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> +##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> +##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> +##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> +##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> +##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> +##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> +##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> +##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT snps |
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| Binary file test-data/test/snps.vcf.gz.tbi has changed |
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| diff -r 000000000000 -r 0801bffdfcc8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Jun 05 21:12:39 2016 -0400 |
| b |
| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="snippy" version="3.0"> + <repository changeset_revision="f8b5ebbd6121" name="package_snippy_3_0" owner="simon-gladman" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="freebayes" version="0.9.20"> + <repository changeset_revision="059e6e3d99cc" name="package_freebayes_0_9_20_b040236" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bwa" version="0.7.12"> + <repository changeset_revision="6af9b24ddeee" name="package_bwa_0_7_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |