Repository 'delly_merge'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/delly_merge

Changeset 0:6331d804f983 (2020-09-28)
Next changeset 1:97c7441aed0d (2020-10-29)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
added:
macros.xml
merge.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
b
diff -r 000000000000 -r 6331d804f983 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Sep 28 07:45:03 2020 +0000
[
@@ -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
b
diff -r 000000000000 -r 6331d804f983 merge.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.xml Mon Sep 28 07:45:03 2020 +0000
[
@@ -0,0 +1,178 @@
+<?xml version="1.0"?>
+<tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+    <description>structural variants across/within VCF/BCF file(s)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize 
+#for $i, $current in enumerate($samples)
+    #if $current.is_of_type('vcf')
+        bcftools view -Ob '$current' > 'sample_${i}.bcf.gz' &&
+        bcftools index 'sample_${i}.bcf.gz' &&
+    #else
+        ln -s '${current}' 'sample_${i}.bcf.gz' &&
+        ln -s '${current.metadata.bcf_index}' 'sample_${i}.bcf.gz.csi' &&
+    #end if
+#end for
+
+## run
+delly merge
+## generic options
+--outfile 'result.bcf'
+--chunks $generic.chunks
+--vaf $generic.vaf
+--coverage $generic.coverage
+--minsize $generic.minsize
+--maxsize $generic.maxsize
+$generic.precise
+$generic.pass
+## overlap options
+--bp-offset $overlap.bpoffset
+--rec-overlap $overlap.recoverlap
+## samples
+#for $i, $current in enumerate($samples)
+    'sample_${i}.bcf.gz'
+#end for
+
+## postprocessing
+#if 'log' in $oo.out
+    |& tee 'log.txt'
+#end if
+#if 'vcf' in $oo.out
+    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
+#end if
+    ]]></command>
+    <inputs>
+        <expand macro="samples" format="bcf,vcf"/>
+        <section name="generic" title="Generic options" expanded="true">
+            <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/>
+            <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
+            <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/>
+            <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
+            <param argument="--maxsize" type="integer" value="1000000" label="Set maximum SV size"/>
+            <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/>
+            <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
+        </section>
+        <section name="overlap" title="Overlap options" expanded="true">
+            <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/>
+            <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/>
+        </section>
+        <section name="oo" title="Output options">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+                <option value="bcf" selected="true">BCF</option>
+                <option value="vcf">VCF</option>
+                <option value="log">Log</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="vcf"/>
+        <expand macro="bcf"/>
+        <expand macro="log"/>
+    </outputs>
+    <tests>
+        <!-- #1 default, bcf -->
+        <test expect_num_outputs="2">
+            <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/>
+            <section name="oo">
+                <param name="out" value="vcf,bcf"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1851" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 bcf-->
+        <test expect_num_outputs="3">
+            <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/>
+            <section name="generic">
+                <param name="chunks" value="500"/>
+                <param name="vaf" value="0.16"/>
+                <param name="coverage" value="10"/>
+                <param name="minsize" value="0"/>
+                <param name="maxsize" value="1000000"/>
+                <param name="precise" value="true"/>
+                <param name="pass" value="true"/>
+            </section>
+            <section name="overlap">
+                <param name="bp-offset" value="1000"/>
+                <param name="rec-overlap" value="0.79"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1851" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                    <has_text_matching expression="chr5&#009;75911568.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done\."/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 default, vcf -->
+        <test expect_num_outputs="2">
+            <param name="samples" value="call_1.vcf.gz,call_2.vcf.gz"/>
+            <section name="oo">
+                <param name="out" value="vcf,bcf"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1851" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+Delly *merge* merges SV sites into a unified site list.
+
+**Input**
+
+BCF or VCF files.
+
+**Output**
+
+A single BCF file.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
b
diff -r 000000000000 -r 6331d804f983 test-data/call_1.bcf.gz
b
Binary file test-data/call_1.bcf.gz has changed
b
diff -r 000000000000 -r 6331d804f983 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 07:45:03 2020 +0000
b
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'
b
diff -r 000000000000 -r 6331d804f983 test-data/call_2.bcf.gz
b
Binary file test-data/call_2.bcf.gz has changed
b
diff -r 000000000000 -r 6331d804f983 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 07:45:03 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 6331d804f983 test-data/exclude.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclude.tsv Mon Sep 28 07:45:03 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 6331d804f983 test-data/genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta Mon Sep 28 07:45:03 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 6331d804f983 test-data/normal.bam
b
Binary file test-data/normal.bam has changed
b
diff -r 000000000000 -r 6331d804f983 test-data/samples.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv Mon Sep 28 07:45:03 2020 +0000
b
@@ -0,0 +1,2 @@
+NORMAL control
+TUMOR tumor
b
diff -r 000000000000 -r 6331d804f983 test-data/tumor.bam
b
Binary file test-data/tumor.bam has changed