| Next changeset 1:9919057a466c (2020-10-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884" |
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added:
filter.xml macros.xml test-data/call_1.bcf.gz test-data/call_1.vcf.gz test-data/call_2.bcf.gz test-data/call_2.vcf.gz test-data/exclude.tsv test-data/genome.fasta test-data/normal.bam test-data/samples.tsv test-data/tumor.bam |
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| diff -r 000000000000 -r a75e05f20a66 filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.xml Mon Sep 28 07:44:40 2020 +0000 |
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| b'@@ -0,0 +1,272 @@\n+<?xml version="1.0"?>\n+<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01">\n+ <description>somatic or germline structural variants</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+## initialize\n+#if $samples.is_of_type(\'vcf\')\n+ bcftools view -Ob \'$samples\' > \'sample.bcf.gz\' &&\n+ bcftools index \'sample.bcf.gz\' &&\n+#else\n+ ln -s \'${samples}\' \'sample.bcf.gz\' &&\n+ ln -s \'${samples.metadata.bcf_index}\' \'sample.bcf.gz.csi\' &&\n+#end if\n+\n+## run\n+delly filter\n+## generic options\n+--filter $sv.mode_cond.mode_sel\n+--outfile \'result.bcf\'\n+--altaf $generic.altaf\n+--minsize $generic.minsize\n+--maxsize $generic.maxsize\n+--ratiogeno $generic.ratiogeno\n+$generic.pass\n+## somatic options\n+#if $sv.mode_cond.mode_sel == \'somatic\'\n+ --samples \'$sv.mode_cond.samples\'\n+ --coverage $sv.mode_cond.coverage\n+ --controlcontamination $sv.mode_cond.controlcontamination\n+#end if\n+## germline options\n+#if $sv.mode_cond.mode_sel == \'germline\'\n+ --gq $sv.mode_cond.gq\n+ --rddel $sv.mode_cond.rddel\n+ --rddup $sv.mode_cond.rddup\n+#end if\n+## samples\n+\'sample.bcf.gz\' ## input\n+\n+## postprocessing\n+#if \'log\' in $oo.out\n+ |& tee \'log.txt\'\n+#end if\n+#if \'vcf\' in $oo.out\n+ && test -f \'result.bcf\' && bcftools view \'result.bcf\' > \'result.vcf\' || echo \'No results.\'\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/>\n+ <section name="generic" title="Generic options" expanded="true">\n+ <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>\n+ <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>\n+ <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/>\n+ <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/>\n+ <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>\n+ </section>\n+ <section name="sv" title="SV calling options" expanded="true">\n+ <conditional name="mode_cond">\n+ <param argument="mode_sel" type="select" label="Select filter mode">\n+ <option value="somatic" selected="true">Somatic</option>\n+ <option value="germline">Germline</option>\n+ </param>\n+ <when value="somatic">\n+ <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>\n+ <param argument="--coverage" type="integer" value="10" label="Set minimum coverage in tumor."/>\n+ <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/>\n+ </when>\n+ <when value="germline">\n+ <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/>\n+ <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/>\n+ <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/>\n+ </when>\n+ </conditional>\n+ </section>\n+ <section name="oo" title="Output options">\n+ <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">\n+ <option value="bcf" selected="true">BCF</option>\n+ '..b' <assert_contents>\n+ <has_n_lines n="139"/>\n+ <has_line line="##fileformat=VCFv4.2"/>\n+ <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- #4 germline, bcf -->\n+ <test expect_num_outputs="3">\n+ <param name="samples" value="call_1.bcf.gz"/>\n+ <section name="generic">\n+ <param name="altaf" value="0.1"/>\n+ <param name="minsize" value="1"/>\n+ <param name="maxsize" value="500000001"/>\n+ <param name="ratiogeno" value="0.76"/>\n+ <param name="pass" value="true"/>\n+ </section>\n+ <section name="sv">\n+ <conditional name="mode_cond">\n+ <param name="mode_sel" value="germline"/>\n+ <param name="gq" value="14"/>\n+ <param name="rddel" value="0.7"/>\n+ <param name="rddup" value="1.3"/>\n+ </conditional>\n+ </section>\n+ <section name="oo">\n+ <param name="out" value="vcf,bcf,log"/>\n+ </section>\n+ <output name="out_bcf">\n+ <assert_contents>\n+ <has_size value="2264" delta="10"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_vcf">\n+ <assert_contents>\n+ <has_n_lines n="139"/>\n+ <has_line line="##fileformat=VCFv4.2"/>\n+ <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_log">\n+ <assert_contents>\n+ <has_text_matching expression=".+Done\\."/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- #5 default, somatic, vcf -->\n+ <test expect_num_outputs="2">\n+ <param name="samples" value="call_1.vcf.gz"/>\n+ <section name="sv">\n+ <conditional name="mode_cond">\n+ <param name="mode_sel" value="somatic"/>\n+ <param name="samples" value="samples.tsv"/>\n+ </conditional>\n+ </section>\n+ <section name="oo">\n+ <param name="out" value="vcf,bcf"/>\n+ </section>\n+ <output name="out_bcf">\n+ <assert_contents>\n+ <has_size value="2440" delta="10"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_vcf">\n+ <assert_contents>\n+ <has_n_lines n="142"/>\n+ <has_line line="##fileformat=VCFv4.2"/>\n+ <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+@WID@\n+\n+Delly *filter* contains workflows for germline and somatic SV calling.\n+\n+**Input**\n+\n+*Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control.\n+\n+*Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes.\n+\n+**Output**\n+\n+The output is available in BCF and VCF format.\n+\n+.. class:: infomark\n+\n+**References**\n+\n+@REFERENCES@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r a75e05f20a66 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 28 07:44:40 2020 +0000 |
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| @@ -0,0 +1,94 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">0.8.3</token> + <token name="@DESCRIPTION@"></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">delly</requirement> + <requirement type="package" version="1.10.2">bcftools</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/bts378</citation> + </citations> + </xml> + + <!-- + input + --> + + <xml name="exclude"> + <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/> + </xml> + <xml name="genome"> + <param argument="--genome" type="data" format="fasta" label="Select genome"/> + </xml> + <xml name="genoqual"> + <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/> + </xml> + <xml name="minclip"> + <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/> + </xml> + <xml name="maxreadsep"> + <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/> + </xml> + <xml name="minrefsep"> + <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/> + </xml> + <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)"> + <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/> + </xml> + <xml name="svtype"> + <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect"> + <option value="ALL" selected="true">All types (ALL)</option> + <option value="DEL">Deletion (DEL)</option> + <option value="INS">Insertion (INS)</option> + <option value="DUP">Duplication (DUP)</option> + <option value="INV">Inversion (INV)</option> + <option value="BND">Translocation (BND)</option> + </param> + </xml> + <xml name="vcffile"> + <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/> + </xml> + + <!-- + output + --> + + <xml name="vcf"> + <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)"> + <filter>'vcf' in oo['out']</filter> + </data> + </xml> + <xml name="bcf"> + <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)"> + <filter>'bcf' in oo['out']</filter> + </data> + </xml> + <xml name="dump"> + <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> + <filter>'dump' in oo['out']</filter> + </data> + </xml> + <xml name="log"> + <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log"> + <filter>'log' in oo['out']</filter> + </data> + </xml> + + <!-- + Help + --> + + <token name="@WID@"><![CDATA[ +Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. + ]]></token> + <token name="@REFERENCES@"><![CDATA[ +More information are available on `github <https://github.com/dellytools/delly>`_. + ]]></token> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r a75e05f20a66 test-data/call_1.bcf.gz |
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| Binary file test-data/call_1.bcf.gz has changed |
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| diff -r 000000000000 -r a75e05f20a66 test-data/call_1.vcf.gz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/call_1.vcf.gz Mon Sep 28 07:44:40 2020 +0000 |
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| b'@@ -0,0 +1,146 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##fileDate=20200728\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=BND,Description="Translocation">\n+##ALT=<ID=INS,Description="Insertion">\n+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">\n+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">\n+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">\n+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">\n+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">\n+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">\n+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">\n+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">\n+##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">\n+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">\n+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">\n+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">\n+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">\n+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">\n+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">\n+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">\n+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">\n+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">\n+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">\n+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">\n+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">\n+##reference=../data/v1/genome.fasta\n+##contig=<ID=chr10,length=135534747>\n+##contig=<ID=chr11,length=135006516>\n+##contig=<ID=chr11_gl000202_random,length=40103>\n+##contig=<ID=chr12,length=133851895>\n+##contig=<ID=chr13,length=115169878>\n+##contig=<ID=chr14,length=107349540>\n+##contig=<ID=chr15,length=102531392>\n+##contig=<ID=chr16,length=90354753>\n+##contig=<ID=chr17_ctg5_hap1,length=1680828>\n+##contig=<ID=chr17,length=81195210>\n+##contig=<ID=chr17_gl000203_random,length=37498>\n+##contig=<ID=chr17_gl000204_random,length=81310>\n+##contig=<ID=chr17_gl000205_ra'..b'54>\n+##contig=<ID=chrUn_gl000247,length=36422>\n+##contig=<ID=chrUn_gl000248,length=39786>\n+##contig=<ID=chrUn_gl000249,length=38502>\n+##contig=<ID=chrX,length=155270560>\n+##contig=<ID=chrY,length=59373566>\n+##bcftools_viewVersion=1.10.2+htslib-1.10.2\n+##bcftools_viewCommand=view -Ov call_1.bcf.gz; Date=Sun Sep 27 02:27:42 2020\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR\n+chr12\t132969151\tDEL00000000\tG\t<DEL>\t107\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=132969179;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=41;INSLEN=0;HOMLEN=19;SR=3;SRQ=1;CONSENSUS=CCCCACTCTCCCCCCGGACCCTCCGGCCACCCTGCTCTCCCCCGGGACCCTCCGACCACGTTGCTCTTCCCAGGGTTCTGGCAC;CE=1.70498\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t1/1:-10.3982,-0.901271,0:10:LowQual:28:44:28:2:0:0:0:3\t0/1:-11.9941,0,-5.30498:53:PASS:92:160:127:1:0:0:2:4\n+chr17\t40726730\tDEL00000001\tC\t<DEL>\t133\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=40726765;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=50;INSLEN=0;HOMLEN=9;SR=3;SRQ=1;CONSENSUS=CTCTCTCCCTCCTTCCTTCCTTCCTTTTTCCTCCCTCCCTCCCTCTTTCTCCCTCCCTTCCCTCTTTTCCTCTCTTTCTTTCTCTGT;CE=1.07866\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t1/1:-7.79989,-0.601951,0:7:LowQual:31:1:20:0:0:0:0:2\t1/1:-6.29935,-0.601408,0:7:LowQual:66:5:34:0:0:0:0:2\n+chr17\t74283142\tDEL00000002\tC\t<DEL>\t145\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74283171;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=50;INSLEN=0;HOMLEN=18;SR=3;SRQ=1;CONSENSUS=CCCACCCCCTGCCCACACACCACATAACACACACACACACACACGATGGGAGGGACCTAGTTTTTGATGAGAGGTGGGAGGGCAGGGCCAAGCCAG;CE=1.91042\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t1/1:-6.99973,-0.601785,0:7:LowQual:28:89:217:1:0:0:0:2\t1/1:-13.3977,-1.20187,0:12:LowQual:28:10:70:0:0:0:0:4\n+chr17\t79612049\tDEL00000003\tA\t<DEL>\t840\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79612086;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=50;INSLEN=0;HOMLEN=8;SR=17;SRQ=1;CONSENSUS=TTCCTCTTCCCTCTGCAGGAAACTGCAGGCCAGAAGCCCCTCTCTGTGCACAGGGAGGACCAGGCGGAGGCCTGGGGCTGCAGCTGCTGTCCCCCGGAGACCAAGCAC;CE=1.9233\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t0/1:-34.0593,0,-106.559:10000:PASS:844:1944:1927:1:0:0:30:12\t0/1:-235.677,0,-181.078:10000:PASS:1973:3537:4588:1:0:0:54:68\n+chr5\t13830007\tDEL00000004\tT\t<DEL>\t135\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=13830038;PE=0;MAPQ=0;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=45;INSLEN=0;HOMLEN=5;SR=3;SRQ=0.987179;CONSENSUS=CTATTCATATGATCTTTGCTTAACACCAAAAGGTTTTCCATTCAAGAAAACAGATGACATATGACCAGGGAGATGCAT;CE=1.93383\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t0/1:-14.6949,0,-2.59501:26:PASS:67:26:69:0:0:0:1:4\t0/1:-3.39797,0,-3.49798:31:PASS:30:37:47:1:0:0:1:1\n+chr5\t74363006\tDEL00000005\tC\t<DEL>\t350\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74363047;PE=0;MAPQ=0;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=50;INSLEN=0;HOMLEN=5;SR=7;SRQ=1;CONSENSUS=AAAGTGGTTTCTTGAGACAAAATCTACTCCTGGTGTGGTGATGTGAACACTTAGATGATAAAGCAGCAGCAGGGTGTAAGAGGATTGACTCCGATTTTCAA;CE=1.95354\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t0/1:-11.1851,0,-39.1848:112:PASS:382:637:460:2:0:0:11:4\t0/1:-12.7889,0,-25.2888:128:PASS:279:415:490:1:0:0:7:4\n+chr5\t75911568\tDEL00000006\tT\t<DEL>\t745\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=75911598;PE=0;MAPQ=0;CT=3to5;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=50;INSLEN=0;HOMLEN=1;SR=15;SRQ=1;CONSENSUS=TGTCTAATCACTAATGTCTTCCTTCCTGTCTAATCACTGAGTTAAGGGAAAAATAGTCATTTACTAATTCCATTTCCCCATTAAAAGCTATGTCTAAGAAAAAAAATAGTGGAGGCATTATTTAAAAC;CE=1.88992\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t0/1:-61.5633,0,-65.3615:10000:PASS:779:810:615:1:0:0:20:18\t0/1:-39.5838,0,-14.884:149:PASS:357:220:320:1:0:0:5:11\n+chr5\t79865393\tDEL00000007\tG\t<DEL>\t150\tPASS\tPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79865420;PE=0;MAPQ=0;CT=3to5;CIPOS=-29,29;CIEND=-29,29;SRMAPQ=50;INSLEN=0;HOMLEN=31;SR=3;SRQ=1;CONSENSUS=CTCCTGCTGCCCAGCTGCCGAGGCACCTGCGGAGACGCGCCCAAGTCAGCCCCTCCGACCCGCGCGCTCTTGCGGCCCAGCGCGCGCCGCT;CE=1.74972\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:12:0:0:0:0:0:0:0\t0/1:-13.9933,0,-8.89295:89:PASS:117:172:133:1:0:0:3:4\n' |
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| diff -r 000000000000 -r a75e05f20a66 test-data/call_2.bcf.gz |
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| Binary file test-data/call_2.bcf.gz has changed |
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| diff -r 000000000000 -r a75e05f20a66 test-data/call_2.vcf.gz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/call_2.vcf.gz Mon Sep 28 07:44:40 2020 +0000 |
| b |
| b'@@ -0,0 +1,120 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##fileDate=20200728\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=BND,Description="Translocation">\n+##ALT=<ID=INS,Description="Insertion">\n+##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">\n+##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">\n+##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">\n+##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">\n+##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">\n+##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">\n+##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">\n+##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">\n+##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">\n+##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">\n+##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">\n+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">\n+##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">\n+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">\n+##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">\n+##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">\n+##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">\n+##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">\n+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">\n+##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">\n+##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">\n+##reference=../data/v4/genome.fasta\n+##contig=<ID=chr16,length=10000000>\n+##bcftools_viewVersion=1.10.2+htslib-1.10.2\n+##bcftools_viewCommand=view -Ov call_2.bcf.gz; Date=Sun Sep 27 02:27:49 2020\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tnormal\n+chr16\t825909\tDEL00000000\tT\t<DEL>\t173\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=827789;PE=5;MAPQ=37;CT=3to5;CIPOS=-125,125;CIEND=-125,125\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t850905\tDEL00000001\tG\t<DEL>\t247\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD='..b'37;CT=3to5;CIPOS=-181,181;CIEND=-181,181\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t8607361\tDEL00000058\tA\t<DEL>\t222\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8608882;PE=6;MAPQ=37;CT=3to5;CIPOS=-68,68;CIEND=-68,68\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t8681669\tDEL00000059\tC\t<DEL>\t148\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8685132;PE=4;MAPQ=37;CT=3to5;CIPOS=-74,74;CIEND=-74,74\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t8824490\tDEL00000060\tG\t<DEL>\t111\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8826563;PE=3;MAPQ=37;CT=3to5;CIPOS=-60,60;CIEND=-60,60\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t8923597\tDEL00000061\tC\t<DEL>\t134\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=8926010;PE=4;MAPQ=37;CT=3to5;CIPOS=-156,156;CIEND=-156,156\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9090265\tDEL00000062\tC\t<DEL>\t148\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9093228;PE=4;MAPQ=37;CT=3to5;CIPOS=-128,128;CIEND=-128,128\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9119366\tDEL00000063\tT\t<DEL>\t74\tLowQual\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9123335;PE=2;MAPQ=37;CT=3to5;CIPOS=-140,140;CIEND=-140,140\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9178997\tDEL00000064\tT\t<DEL>\t185\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9182500;PE=5;MAPQ=37;CT=3to5;CIPOS=-66,66;CIEND=-66,66\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9226404\tDEL00000065\tT\t<DEL>\t111\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9227636;PE=3;MAPQ=37;CT=3to5;CIPOS=-127,127;CIEND=-127,127\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9319688\tDEL00000066\tC\t<DEL>\t111\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9320353;PE=3;MAPQ=37;CT=3to5;CIPOS=-133,133;CIEND=-133,133\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9359380\tDEL00000067\tA\t<DEL>\t333\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9361199;PE=9;MAPQ=37;CT=3to5;CIPOS=-80,80;CIEND=-80,80\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9501567\tDEL00000068\tG\t<DEL>\t247\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9504493;PE=7;MAPQ=37;CT=3to5;CIPOS=-62,62;CIEND=-62,62\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9596261\tDEL00000069\tA\t<DEL>\t370\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9599737;PE=10;MAPQ=37;CT=3to5;CIPOS=-64,64;CIEND=-64,64\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9670189\tDEL00000070\tA\t<DEL>\t185\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9673420;PE=5;MAPQ=37;CT=3to5;CIPOS=-145,145;CIEND=-145,145\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9721367\tDEL00000071\tT\t<DEL>\t370\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9723693;PE=10;MAPQ=37;CT=3to5;CIPOS=-62,62;CIEND=-62,62\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9754516\tDEL00000072\tT\t<DEL>\t284\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9757726;PE=8;MAPQ=37;CT=3to5;CIPOS=-50,50;CIEND=-50,50\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n+chr16\t9894428\tDEL00000073\tT\t<DEL>\t148\tPASS\tIMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=9898668;PE=4;MAPQ=37;CT=3to5;CIPOS=-91,91;CIEND=-91,91\tGT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV\t./.:0,0,0:0:LowQual:0:746617080:32642:45746:0:0:0:0\n' |
| b |
| diff -r 000000000000 -r a75e05f20a66 test-data/exclude.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/exclude.tsv Mon Sep 28 07:44:40 2020 +0000 |
| b |
| @@ -0,0 +1,267 @@ +chr1 0 10000 telomere +chr1 121535434 124535434 centromere +chr1 249240621 249250621 telomere +chr10 0 10000 telomere +chr10 39254935 42254935 centromere +chr10 135524747 135534747 telomere +chr11 0 10000 telomere +chr11 51644205 54644205 centromere +chr11 134996516 135006516 telomere +chr12 0 10000 telomere +chr12 34856694 37856694 centromere +chr12 133841895 133851895 telomere +chr13 0 10000 telomere +chr13 16000000 19000000 centromere +chr13 115159878 115169878 telomere +chr14 0 10000 telomere +chr14 16000000 19000000 centromere +chr14 107339540 107349540 telomere +chr15 0 10000 telomere +chr15 17000000 20000000 centromere +chr15 102521392 102531392 telomere +chr16 0 10000 telomere +chr16 35335801 38335801 centromere +chr16 46380000 46450000 lowcomplexity +chr16 90344753 90354753 telomere +chr17 22263006 25263006 centromere +chr18 0 10000 telomere +chr18 15460898 18460898 centromere +chr18 78067248 78077248 telomere +chr19 0 10000 telomere +chr19 24681782 27681782 centromere +chr19 59118983 59128983 telomere +chr2 0 10000 telomere +chr2 33141000 33142000 lowcomplexity +chr2 92326171 95326171 centromere +chr2 243189373 243199373 telomere +chr20 0 10000 telomere +chr20 26369569 29369569 centromere +chr20 63015520 63025520 telomere +chr21 0 10000 telomere +chr21 11288129 14288129 centromere +chr21 48119895 48129895 telomere +chr22 0 10000 telomere +chr22 13000000 16000000 centromere +chr22 51294566 51304566 telomere +chr3 0 10000 telomere +chr3 90504854 93504854 centromere +chr3 198012430 198022430 telomere +chr4 0 10000 telomere +chr4 49660117 52660117 centromere +chr4 191144276 191154276 telomere +chr5 0 10000 telomere +chr5 46405641 49405641 centromere +chr5 180905260 180915260 telomere +chr6 0 10000 telomere +chr6 58830166 61830166 centromere +chr6 171105067 171115067 telomere +chr7 0 10000 telomere +chr7 58054331 61054331 centromere +chr7 159128663 159138663 telomere +chr8 0 10000 telomere +chr8 43793000 46857000 centromere +chr8 146354022 146364022 telomere +chr9 0 10000 telomere +chr9 47367679 50367679 centromere +chr9 141203431 141213431 telomere +chrX 0 10000 telomere +chrX 58632012 61632012 centromere +chrX 155260560 155270560 telomere +chrY 0 10000 telomere +chrY 10104553 13104553 centromere +chrY 59363566 59373566 telomere +1 0 10000 telomere +1 121535434 124535434 centromere +1 249240621 249250621 telomere +10 0 10000 telomere +10 39254935 42254935 centromere +10 135524747 135534747 telomere +11 0 10000 telomere +11 51644205 54644205 centromere +11 134996516 135006516 telomere +12 0 10000 telomere +12 34856694 37856694 centromere +12 133841895 133851895 telomere +13 0 10000 telomere +13 16000000 19000000 centromere +13 115159878 115169878 telomere +14 0 10000 telomere +14 16000000 19000000 centromere +14 107339540 107349540 telomere +15 0 10000 telomere +15 17000000 20000000 centromere +15 102521392 102531392 telomere +16 0 10000 telomere +16 35335801 38335801 centromere +16 46380000 46450000 lowcomplexity +16 90344753 90354753 telomere +17 22263006 25263006 centromere +18 0 10000 telomere +18 15460898 18460898 centromere +18 78067248 78077248 telomere +19 0 10000 telomere +19 24681782 27681782 centromere +19 59118983 59128983 telomere +2 0 10000 telomere +2 33141000 33142000 lowcomplexity +2 92326171 95326171 centromere +2 243189373 243199373 telomere +20 0 10000 telomere +20 26369569 29369569 centromere +20 63015520 63025520 telomere +21 0 10000 telomere +21 11288129 14288129 centromere +21 48119895 48129895 telomere +22 0 10000 telomere +22 13000000 16000000 centromere +22 51294566 51304566 telomere +3 0 10000 telomere +3 90504854 93504854 centromere +3 198012430 198022430 telomere +4 0 10000 telomere +4 49660117 52660117 centromere +4 191144276 191154276 telomere +5 0 10000 telomere +5 46405641 49405641 centromere +5 180905260 180915260 telomere +6 0 10000 telomere +6 58830166 61830166 centromere +6 171105067 171115067 telomere +7 0 10000 telomere +7 58054331 61054331 centromere +7 159128663 159138663 telomere +8 0 10000 telomere +8 43793000 46857000 centromere +8 146354022 146364022 telomere +9 0 10000 telomere +9 47367679 50367679 centromere +9 141203431 141213431 telomere +X 0 10000 telomere +X 58632012 61632012 centromere +X 155260560 155270560 telomere +Y 0 10000 telomere +Y 10104553 13104553 centromere +Y 59363566 59373566 telomere +chrM +chrMT +MT +GL000207.1 +GL000226.1 +GL000229.1 +GL000231.1 +GL000210.1 +GL000239.1 +GL000235.1 +GL000201.1 +GL000247.1 +GL000245.1 +GL000197.1 +GL000203.1 +GL000246.1 +GL000249.1 +GL000196.1 +GL000248.1 +GL000244.1 +GL000238.1 +GL000202.1 +GL000234.1 +GL000232.1 +GL000206.1 +GL000240.1 +GL000236.1 +GL000241.1 +GL000243.1 +GL000242.1 +GL000230.1 +GL000237.1 +GL000233.1 +GL000204.1 +GL000198.1 +GL000208.1 +GL000191.1 +GL000227.1 +GL000228.1 +GL000214.1 +GL000221.1 +GL000209.1 +GL000218.1 +GL000220.1 +GL000213.1 +GL000211.1 +GL000199.1 +GL000217.1 +GL000216.1 +GL000215.1 +GL000205.1 +GL000219.1 +GL000224.1 +GL000223.1 +GL000195.1 +GL000212.1 +GL000222.1 +GL000200.1 +GL000193.1 +GL000194.1 +GL000225.1 +GL000192.1 +NC_007605 +hs37d5 +chr11_gl000202_random +chr17_gl000203_random +chr17_gl000204_random +chr17_gl000205_random +chr17_gl000206_random +chr18_gl000207_random +chr19_gl000208_random +chr19_gl000209_random +chr1_gl000191_random +chr1_gl000192_random +chr21_gl000210_random +chr4_gl000193_random +chr4_gl000194_random +chr7_gl000195_random +chr8_gl000196_random +chr8_gl000197_random +chr9_gl000198_random +chr9_gl000199_random +chr9_gl000200_random +chr9_gl000201_random +chrUn_gl000211 +chrUn_gl000212 +chrUn_gl000213 +chrUn_gl000214 +chrUn_gl000215 +chrUn_gl000216 +chrUn_gl000217 +chrUn_gl000218 +chrUn_gl000219 +chrUn_gl000220 +chrUn_gl000221 +chrUn_gl000222 +chrUn_gl000223 +chrUn_gl000224 +chrUn_gl000225 +chrUn_gl000226 +chrUn_gl000227 +chrUn_gl000228 +chrUn_gl000229 +chrUn_gl000230 +chrUn_gl000231 +chrUn_gl000232 +chrUn_gl000233 +chrUn_gl000234 +chrUn_gl000235 +chrUn_gl000236 +chrUn_gl000237 +chrUn_gl000238 +chrUn_gl000239 +chrUn_gl000240 +chrUn_gl000241 +chrUn_gl000242 +chrUn_gl000243 +chrUn_gl000244 +chrUn_gl000245 +chrUn_gl000246 +chrUn_gl000247 +chrUn_gl000248 +chrUn_gl000249 |
| b |
| diff -r 000000000000 -r a75e05f20a66 test-data/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Mon Sep 28 07:44:40 2020 +0000 |
| b |
| b'@@ -0,0 +1,333 @@\n+>chrM\n+NNNCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC\n+CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT\n+TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA\n+TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC\n+GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC\n+CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA\n+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA\n+ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC\n+AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG\n+GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC\n+ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT\n+TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC\n+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT\n+TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA\n+CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC\n+ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC\n+CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA\n+GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA\n+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC\n+TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT\n+AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG\n+TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT\n+ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT\n+GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC\n+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA\n+GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG\n+AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT\n+CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC\n+CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG\n+CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA\n+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT\n+CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA\n+GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC\n+GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT\n+ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT\n+TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG\n+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA\n+GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA\n+AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT\n+GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA\n+TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA\n+GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA\n+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG\n+GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT\n+TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC\n+CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca\n+taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt\n+tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg\n+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA\n+ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA\n+TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA\n+GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT\n+CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC\n+CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT\n+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA\n+TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT\n+CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC\n+TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT\n+TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg\n+taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct\n+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA\n+TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA\n+CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC\n+CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA\n+CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC\n+GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT\n+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT\n+CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC\n+GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT\n+CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC\n+TTATCACAACACAAGAACACC'..b'TTAGTTACCGCTAACAACCTATT\n+CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA\n+TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA\n+GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG\n+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA\n+ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA\n+GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA\n+AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG\n+CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA\n+CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC\n+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT\n+CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA\n+CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT\n+ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG\n+ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC\n+TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG\n+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA\n+ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC\n+TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC\n+CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA\n+AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC\n+ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT\n+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA\n+ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT\n+TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC\n+CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC\n+TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC\n+TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT\n+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC\n+CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT\n+TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG\n+CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT\n+ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA\n+CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA\n+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA\n+ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA\n+AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA\n+TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA\n+GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT\n+CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA\n+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG\n+ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT\n+CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT\n+CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA\n+GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA\n+CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA\n+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC\n+CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT\n+CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT\n+GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC\n+GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA\n+CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT\n+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC\n+GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT\n+CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT\n+TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC\n+GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT\n+CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC\n+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA\n+GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG\n+CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC\n+TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA\n+CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC\n+TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA\n+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG\n+GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA\n+GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA\n+CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT\n+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC\n+TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT\n+AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC\n+AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG\n+ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC\n+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC\n+CTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r a75e05f20a66 test-data/normal.bam |
| b |
| Binary file test-data/normal.bam has changed |
| b |
| diff -r 000000000000 -r a75e05f20a66 test-data/samples.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tsv Mon Sep 28 07:44:40 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +NORMAL control +TUMOR tumor |
| b |
| diff -r 000000000000 -r a75e05f20a66 test-data/tumor.bam |
| b |
| Binary file test-data/tumor.bam has changed |