| Next changeset 1:59eca98715b4 (2015-12-21) |
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Commit message:
Uploaded |
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added:
phe_samtools_mpileup.sh phe_samtools_mpileup.xml test-data/in_short.sam test-data/out.vcf test-data/ref.fa tool_dependencies.xml |
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| diff -r 000000000000 -r c91df5df0faf phe_samtools_mpileup.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe_samtools_mpileup.sh Mon Dec 21 07:12:34 2015 -0500 |
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| @@ -0,0 +1,22 @@ +#!/bin/bash + +echo $@ + +SAM=$1 +shift +REF=$1 +shift +OUTVCF=$1 + +TMPBAM=$$.tmpbam +TMPBAM2=$$.tmpbam2 + +samtools view -bS $SAM > $TMPBAM +samtools sort $TMPBAM $TMPBAM2 + +CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $TMPBAM2.bam | bcftools call -m -f GQ > $OUTVCF" + +echo "CMD: "$CMD +eval $CMD +rm $TMPBAM +rm $TMPBAM2.bam |
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| diff -r 000000000000 -r c91df5df0faf phe_samtools_mpileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phe_samtools_mpileup.xml Mon Dec 21 07:12:34 2015 -0500 |
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| @@ -0,0 +1,32 @@ +<tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0"> + <description>PHE SNP and indel caller</description> + <requirements> + <requirement type="package" version="1.1">samtools</requirement> + </requirements> + <command interpreter="bash"> + phe_samtools_mpileup.sh $input_sam $ref_file $outvcf + </command> + <inputs> + <param name="input_sam" type="data" format="sam" label="SAM file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </inputs> + <outputs> + <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" /> + </outputs> + <tests> + <test> + <param name="in_sam" value="in_short.sam" ftype="sam" /> + <param name="ref_file" value="ref.fa" ftype="fasta" /> + <output name="outvcf" file="out.vcf" ftype="vcf" /> + </test> + </tests> + <help> + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</tool> |
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| diff -r 000000000000 -r c91df5df0faf test-data/in_short.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_short.sam Mon Dec 21 07:12:34 2015 -0500 |
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| b"@@ -0,0 +1,10000 @@\n+@SQ\tSN:gi|15829254|ref|NC_002695.1|\tLN:5498450\n+@RG\tID:test_sample\tSM:test_sample\n+@PG\tID:bwa\tPN:bwa\tVN:0.7.12-r1039\tCL:bwa mem -R @RG\\tID:test_sample\\tSM:test_sample -t 1 ref.fa r1.fastq r2.fastq\n+HWI-D00151:47:H7926ADXX:1:1101:1645:2045\t83\tgi|15829254|ref|NC_002695.1|\t5459580\t60\t100M\t=\t5459536\t-144\tGCATCGGGTTGCCAGTCCGGATACATGGCGAATTTCCCCATGGGTACAGCAACGGGAGCGGCTTGCGGTTCCTGATAGAGTTGATCGTCCAGATCGACAN\tFFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFBFFFFFFFFFFFFIIIIIIIIIFFIIIIIIIIIIIFIFIIIIIIFIIFFFFFFFFFB<0#\tNM:i:1\tMD:Z:99T0\tAS:i:99\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:1645:2045\t163\tgi|15829254|ref|NC_002695.1|\t5459536\t60\t100M\t=\t5459580\t144\tCTCTTAGCGCCACGCCCCATAGAGCCGCCAGGCGGATAAAGTCGGCATCGGGTTGCCAGTCCGGATACATGGCGAATTTCCCCATGGGTACAGCAACGGG\tBBBFFFFFFFFFFFFIIIIIFIIIIIFIIIFIFFIBFFFFFFFFBFBBBBFFFBFBFFFFFFFFBBBFBBFFBFBFFFFFFFFBBFBFBFFBBBBBBBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:1584:2047\t83\tgi|15829254|ref|NC_002695.1|\t1794502\t60\t100M\t=\t1794386\t-216\tGAAATTATTAGCACCACAGTCAGTTTGTGAAAATGTGAAGATATTCAGAAGTTTTATTCAGTCATGATACAGGCATCCTCCGGGATGCCTGTTGTTTTTN\tBFFFFBBBFFFFFFFFFFFFFFBFFFFFFFFFFFFFIIIIIIIIIFIFIIIFIIIIIFIIIIFBIIFFFFFBIIIFIFBIIIIIIIIFFFFFFFFFF<0#\tNM:i:1\tMD:Z:99G0\tAS:i:99\tXS:i:37\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:1584:2047\t163\tgi|15829254|ref|NC_002695.1|\t1794386\t60\t96M\t=\t1794502\t216\tGGGCGGCAGAGGGAAAAAGAATAAAAAAATCCCGCAGAGTTGCGGGGACAGACAAAGATTAACGTTAAGGAGGTATTTTTGTTTCTGGTGCTCGGG\tB<BFFFBBFFFF'0BFFFFFFBFFFIIIFIFFFFFFFBB'<BBBBB<777<7770<B<<<<<'77007<BB<0<<<FFFBB<BB0<<B<<'00<<B\tNM:i:2\tMD:Z:12T59T23\tAS:i:86\tXS:i:22\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:1733:2205\t83\tgi|15829254|ref|NC_002695.1|\t3503961\t60\t100M\t=\t3503681\t-380\tAACACATTGTCTGCCACGTGATTGTGGATGGAGAATGCACCTTCACTATTCGTACCGCTCACCGTCGTACCGTTAGTGTTAGTTTTTAAAATTGCACCAT\tFFFBFFBFFFFFFFFFFFFFFBBFFFBFFFFFFFFFFFFFFFFFFFFFFFFIFFIIFIFFFIFIFIIFFIIIIIIIIIFIIIIIIFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:1733:2205\t163\tgi|15829254|ref|NC_002695.1|\t3503681\t60\t100M\t=\t3503961\t380\tGGATATAATTGTTGTGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGT\tBBBFFFFFFFFFFIIIIIIIIFIIIIIIIIIIIIIIIFIIIIIIIIIIIFFFIIFFFFBFFFFFFFBFFFFFFFFFFFFFBBBFFFFFFFFBFBBFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:2088:2189\t99\tgi|15829254|ref|NC_002695.1|\t1652878\t60\t100M\t=\t1653052\t274\tCTGTAGATCTGGAAATCGCAACGGAGGAAGAAACCTCATTGCTGGAAGCCTGGAAAAAGTATCGGGTGTTGCTGAACCGTGTTGATACATCAACTGCACC\t7BBBFFFFFFFFFFIFIIIIFFFIFIFFBFBFBFFFFFFFIIIIFBBFIIFIFIIFBFFBBFBBBFBBBBBFFFBBBFFBB<BBFFBBFFBBBFFFFFFB\tNM:i:1\tMD:Z:32G67\tAS:i:95\tXS:i:86\tRG:Z:test_sample\tXA:Z:gi|15829254|ref|NC_002695.1|,-3476634,100M,3;\n+HWI-D00151:47:H7926ADXX:1:1101:2088:2189\t147\tgi|15829254|ref|NC_002695.1|\t1653052\t60\t100M\t=\t1652878\t-274\tAATGTATTTTCAGAGGCTAGAGCTTAGGATATCTCAGCGGCAATTAACTTATGAGGGATAGCTAAATACCAGAAGATAATTAGTTTTTACTATTTATCTT\tFFBBBBBBBBFBFFFB<FFFFFFBIFFBFFFBF7FFIIIFFFFIFFBIIIIIIIFFFFFIIIFFBFFBIIIIIIIIFFIFFIIIIFFFBFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:2359:2127\t99\tgi|15829254|ref|NC_002695.1|\t1862580\t60\t100M\t=\t1862674\t194\tGCGTTAATTAACCAGCGCCCTAAACCCGGCCAGCTAAAAACCATTTCGGTGATCATCGCCAGCGTCAGCATGGTGGAAAACTGTAAGCCCAGGCGAGGAA\tBBBFFFFFFFFFFIFFFIIFIIFBFFFFBFFFIIIFIIIIBFIIIIIBBFFFFFFFFFFFFFBFFFFBFFFFF<BFBBBFFFFFFFFFFFFFFFFFFFFB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:2359:2127\t147\tgi|15829254|ref|NC_002695.1|\t1862674\t60\t100M\t=\t1862580\t-194\tGAGGAATACCCGGCGGTAACGCGTTATGCAGAACGTGGCGACGCAAAATAGTAAAGCGCGACAAACCGCGGGTCGCCGCCGCTTTTACATAGTTCTGGTC\tFFFFFB<0'<<BFFFB<77<BBBFBFBFFBBB<BFFFBB7'BBBFFB<BBBBFBBB77BBBBB<<FBFBFFFFFFIF<IIIIIIIIFFFFFFFFFFFBBB\tNM:i:1\tMD:Z:8A91\tAS:i:95\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:2473:2147\t99\tgi|15829254|ref|NC_002695.1|\t2921256\t40\t100M\t=\t2921378\t222\tGGGAAACCCTGTCCAGCAACTGCAGGAACCAGTAGCCCGTTCCCACCGCTGACGTGGTGTATGACAC"..b"BBFFFFIIFIIIIFFFIIFIIFBBFFFFFFFBBBBBBBBBB<<BBBBBBBFBBFBBBBBBBBBBBBBBB<BBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6072:14609\t147\tgi|15829254|ref|NC_002695.1|\t3592550\t60\t77M\t=\t3592174\t-453\tACGGTATGAGCAATGGCATTTTTGCCCGGTTCGGCACGTTTCATAGTATCGCGCACTGGTGCGGCTAGGATCCCTCC\tB77'<BB<<0<<00<'BBB77B<<770<7B7BFB<0BBFBB7BFFFBFFB7FBFBFIIFFBBFFBBFFF<B7<F0<B\tNM:i:0\tMD:Z:77\tAS:i:77\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6140:14618\t99\tgi|15829254|ref|NC_002695.1|\t217729\t60\t100M\t=\t217827\t198\tACCCTTCAGAAACCCAGGAGCGTATGATGCTGCGCCTGCTGGCGTGGCTGAAATATGCTGATGAACGTCTGCAATTTACCCGTGGTTTGTGTGCCGATGA\tBBBFFFFFFFFFFIIIIIFFFIFIIIIIIIIIIIIIIIIIIIIIIIIFIIFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFBFFBBFFBFFFFBFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6140:14618\t147\tgi|15829254|ref|NC_002695.1|\t217827\t60\t100M\t=\t217729\t-198\tGATGAGCCGGAAGCGTGGCTGCGTAACGATCACCTGGGCATTGATTTGTGGATTGAGCTGGGGCTGCCGGATGAGCGACGAATTAAGAAAGCCTGCACCC\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<FFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6059:14667\t99\tgi|15829254|ref|NC_002695.1|\t1826409\t60\t100M\t=\t1826576\t267\tTCACGGTACTCTACCGTTGGCCTCACTCGTTACTTAGCAATGCCCCGGCTCCACAAACGACGAATATTTTCAGCCATCTTCTTTTACCCTCCACGTCATC\tBBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6059:14667\t147\tgi|15829254|ref|NC_002695.1|\t1826576\t60\t100M\t=\t1826409\t-267\tCAATTTACGTCGGTAGATGTTTTACGGATGCAGAAATTTTATCTGCCGCGTAAAAAGTCTTCGTTTTACCGGCCTGATACTTTTTTGCAATGGGGTGGAC\tFFFFFB<FBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBBBFFFFFFFIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFFIFIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6354:14617\t83\tgi|15829254|ref|NC_002695.1|\t3190027\t60\t100M\t=\t3189766\t-361\tTGAAGATCCAAGTTTTATCTTCGATAAAATATCACACAAACTCAGACATACGGTAACGGAATTCGATGAGAGCGGGAAAAGCGAACCAACGGGCTTATTT\tBB<BB<BBFBFFFFFFBBFFFFFFFFFBFB<BBBBFFBBBBBFFFFFFFBIIIIFFIIIFBBBB<FBFIIIFFFIIIIFIFFFFFFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6354:14617\t163\tgi|15829254|ref|NC_002695.1|\t3189766\t60\t100M\t=\t3190027\t361\tTGACAACATAGTTGAGAAGACTCATGATGATATAAATAATGCTGAATTTACTGATGGTGGTATTGATGATCGTAGTGATATTGGCATTGACTCCAATGAT\tB<BFBFBFFFBFBF<<FBFFII<FFI0BB<B7B0FFFFFIFBBFF<FFFFFBFBFFI7BF7B<BF<FFFFFI77<<BBB<BBFFFB<BBF0BBB<<B<BB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6396:14642\t83\tgi|15829254|ref|NC_002695.1|\t5190286\t60\t100M\t=\t5190150\t-236\tTGCAGTAGAGGAAGGCAATGGTAGTAACCGCCAGATATGCCGGGCGTGCTTTACCAAAGTGACCGTGTCCGAGCAGCAGTAACGCCGCACAGGTGTAAAG\tFFFFBFFFFFFFFFFFFFFFFFFFBBBFBBBFFFFBBFBBBFFFFFFFFFFFBFFFFFFFIIIIIFIIFFFBFFFFFFIIFIFFFFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:6396:14642\t163\tgi|15829254|ref|NC_002695.1|\t5190150\t60\t100M\t=\t5190286\t236\tTTGCTTATTGGTGCATCTAAGGGATACGGGTTTTTATGCAGCCGGTTGTAATTCAGCGCATACATGGCGGTGATGACCATCAGGGTGACAAATGACCACA\tBBBFFFFFBFFFFIFFFIIIFIIFFFIIIIBFFFIFFFFFBFFIIFFFFFFIIIIBFIFBBFFFFFFBFB<B7<07<<BBBBBBB7B0<BFBB<0'<<7B\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:7030:14541\t99\tgi|15829254|ref|NC_002695.1|\t3843633\t60\t100M\t=\t3843936\t403\tCCTTCCGGGAATCGCCATGCCACCGAAAATCCTAATTCCTGGAATTCGTCGATGTGCATTTTTTTACGCAGACGACGGCTACGGTTCTTTGCCATTATTT\tBBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFFIFFFIIIIIIIFFFFFIFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n+HWI-D00151:47:H7926ADXX:1:1101:7030:14541\t147\tgi|15829254|ref|NC_002695.1|\t3843936\t60\t100M\t=\t3843633\t-403\tGCTGCAGTTTGCTTTTTACCAGTTCGGCAAACGGCACCTGAACGATACGGCGTTTATTATGGCGCGCTTTGTGCCACGGGTCAGGGAAAAAGAGCTGCAC\tFFFFFFFFFFFFFFFFBBBFFFFBFFFFFFBFFBBBBBFFBBFBBBFFFFFIIIIFIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n" 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| diff -r 000000000000 -r c91df5df0faf test-data/out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.vcf Mon Dec 21 07:12:34 2015 -0500 |
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| b'@@ -0,0 +1,755984 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##samtoolsVersion=1.1+htslib-1.1\n+##samtoolsCommand=samtools mpileup -t DP,DV,DP4,DPR,SP -Auf ref.fa in_short.bam\n+##reference=file://ref.fa\n+##contig=<ID=gi|15829254|ref|NC_002695.1|,length=5498450>\n+##ALT=<ID=X,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">\n+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">\n+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">\n+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Phred-scaled Genotype Quality">\n+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">\n+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">\n+##bcftools_callVersion=1.1+htslib-1.1\n+##bcftools_callCommand=call -m -f GQ\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest_sample\n+gi|15829254|ref|NC_002695.1|\t32\t.\tG\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t33\t.\tT\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t34\t.\tC\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t35\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t36\t.\tC\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t37\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t38\t.\tG\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15829254|ref|NC_002695.1|\t39\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=1,0,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:1,0,0,0:1\n+gi|15'..b'SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497487\t.\tC\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497488\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497489\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497490\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497491\t.\tC\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497492\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497493\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497494\t.\tC\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497495\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497496\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497497\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497498\t.\tT\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497499\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497500\t.\tA\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497501\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497502\t.\tC\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497503\t.\tG\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497504\t.\tT\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497505\t.\tG\t.\t70\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497506\t.\tG\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497507\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497508\t.\tG\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497509\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497510\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497511\t.\tT\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497512\t.\tC\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497513\t.\tC\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497514\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497515\t.\tA\t.\t67\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497516\t.\tT\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497517\t.\tT\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n+gi|15829254|ref|NC_002695.1|\t5497518\t.\tG\t.\t63\t.\tDP=1;MQ0F=0;AN=2;DP4=0,1,0,0;MQ=60\tGT:DP:DV:SP:DP4:DPR\t0/0:1:0:0:0,1,0,0:1\n' |
| b |
| diff -r 000000000000 -r c91df5df0faf test-data/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Mon Dec 21 07:12:34 2015 -0500 |
| b |
| b'@@ -0,0 +1,78552 @@\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'GGTTAACGTTGCTG\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+\n' |
| b |
| diff -r 000000000000 -r c91df5df0faf tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 21 07:12:34 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.1"> + <repository changeset_revision="f0c7bc0159e9" name="package_samtools_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |