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Changeset 0:00cab3d2e98b (2018-08-15)

Next changeset 1:2ba5317566c0 (2018-10-12)

Commit message:
planemo upload

added:
svtyper.xml
test-data/out.vcf
test-data/test1.bam
test-data/test1.bam.bai
test-data/test1.bam.json
test-data/test1.out.vcf
test-data/test1.vcf

diff -r 000000000000 -r 00cab3d2e98b svtyper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/svtyper.xml Wed Aug 15 15:40:54 2018 -0400

[

b'@@ -0,0 +1,246 @@\n+<tool id="svtyper"\n+ name="svtyper"\n+ version="0.1.0">\n+\n+ <description>Compute variant genotypes</description>\n+\n+ <requirements>\n+ <requirement type="package" version="0.6.1">svtyper</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ </requirements>\n+\n+ <version_command>\n+ svtyper -h | grep version | cut -d \'v\' -f 3\n+ </version_command>\n+\n+ <command detect_errors="aggressive">\n+ <![CDATA[\n+ #set refln = "ref.fasta"\n+ #if $ref\n+ samtools faidx \'$ref\' &&\n+ ln -s -f \'$ref\' \'$refln\' &&\n+ ln -s -f \'${ref}.fai\' \'${refln}.fai\' &&\n+ #end if\n+\n+ #set agnostic_files = []\n+ #for $i, $aln in enumerate( $alignment_files ):\n+ #if $aln\n+ #if $aln.is_of_type("bam"):\n+ ln -s -f \'${aln}\' \'${i}.bam\' &&\n+ ln -s -f \'${aln.metadata.bam_index}\' \'${i}.bam.bai\' &&\n+ $agnostic_files.append(str($i) + ".bam")\n+ #else:\n+ ln -s -f \'${aln}\' \'${i}.cram\' &&\n+ ln -s -f \'${aln.metadata.cram_index}\' \'${i}.cram.crai\' &&\n+ $agnostic_files.append(str($i) + ".cram")\n+ #end if\n+ #end if\n+ #end for\n+\n+ svtyper\n+ -i \'$vcf\'\n+ -B ${",".join(map(str, $agnostic_files))}\n+ -o \'$vcfout\'\n+\n+ #if $ref\n+ -T $refln\n+ #end if\n+\n+ #if $libin\n+ -l $libin\n+ #elif $outputlib\n+ -l $libout\n+ #end if\n+\n+ -m \'$minaln\'\n+ -n \'$samplesize\'\n+\n+ #if int($maxreads) > 0\n+ --max_reads \'$maxreads\'\n+ #end if\n+\n+ --split_weight \'$splitweight\'\n+ --disc_weight \'$discweight\'\n+\n+ #if $outputbam\n+ -w \'$bamout\'\n+ #end if\n+\n+ > \'$vcfout\'\n+ ]]>\n+ </command>\n+\n+ <inputs>\n+ <param name="vcf"\n+ label="vcf file"\n+ argument="--input_vcf"\n+\n+ type="data"\n+ format="vcf"\n+\n+ help="VCF input (default: stdin)"/>\n+\n+ <param name="alignment_files"\n+ label="bam/cram file"\n+ argument="--bam"\n+\n+ type="data"\n+ format="bam,cram"\n+ multiple="true"\n+\n+ help="BAM or CRAM file(s), comma-separated if genotyping multiple samples" />\n+\n+ <param name="ref"\n+ label="Reference"\n+ argument="--ref_fasta"\n+\n+ type="data"\n+ format="fasta"\n+ optional="true"\n+\n+ help="Indexed reference FASTA file (recommended for reading CRAM files)" />\n+\n+ <param name="libin"\n+ label="Library json file"\n+ argument="--lib_info"\n+\n+ type="data"\n+ format="json"\n+\n+ help="read JSON file of library information" />\n+\n+ <param name="minaln"\n+ label="Min aligned bases"\n+ argument="--min_aligned"\n+\n+ type="integer"\n+ value="20"\n+\n+ help="minimum number of aligned bases to consider read as evidence [20]" />\n+\n+ <param name="samplesize"\n+ label="Sampling size for insert size determination"\n+ argument="-n"\n+\n+ type="integer"\n+ value="1000000"\n+\n+ help="number of reads to sample from BAM file for building insert size distribution [1000000]" />\n+\n+ <param name="sumquals"\n+ label="Add genotyping quality"\n+ argument="--sum_quals"\n+\n+ type="boolean"\n+ truevalue="-q"\n+ falsevalue=""\n+ checked="no"\n+ value="false"\n+\n+ help="add genotyping qualit'..b' value="0"\n+\n+ help="maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: 0 = unlimited)" />\n+\n+ <param name="splitweight"\n+ label="Split read weight"\n+ argument="--split_weight"\n+\n+ type="float"\n+ value="1"\n+\n+ help="weight for split reads [1]" />\n+\n+ <param name="discweight"\n+ label="Discordant read weight"\n+ argument="--disc_weight"\n+\n+ type="float"\n+ value="1"\n+\n+ help="weight for discordant paired-end reads [1]" />\n+\n+ <param name="outputlib"\n+ label="Create an output library json file"\n+\n+ type="boolean"\n+ checked="no"\n+\n+ help="if an input library json file (--lib_info) is not provided, create an output library json file" />\n+\n+ <param name="outputbam"\n+ label="Create an output bam file"\n+\n+ type="boolean"\n+ checked="no"\n+\n+ help="generate an output bam file containing the reads supporting the structural variants" />\n+ </inputs>\n+\n+ <outputs>\n+ <data format="vcf" name="vcfout" />\n+ <data format="json" name="libout">\n+ <filter>outputlib</filter>\n+ </data>\n+ <data format="bam" name="bamout">\n+ <filter>outputbam</filter>\n+ </data>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="vcf" value="test1.vcf"/>\n+ <param name="alignment_files" value="test1.bam"/>\n+ <param name="libin" value="test1.bam.json"/>\n+ <output name="vcfout" file="test1.out.vcf"\n+ compare="diff" lines_diff="2" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+ usage: svtyper [-h] [-i FILE] [-o FILE] -B FILE [-T FILE] [-l FILE] [-m INT]\n+ [-n INT] [-q] [--max_reads INT] [--split_weight FLOAT]\n+ [--disc_weight FLOAT] [-w FILE] [--verbose]\n+\n+ svtyper\n+ author: Colby Chiang (colbychiang@wustl.edu)\n+ version: v0.6.0\n+ description: Compute genotype of structural variants based on breakpoint depth\n+\n+ optional arguments:\n+ -h, --help show this help message and exit\n+ -i FILE, --input_vcf FILE\n+ VCF input (default: stdin)\n+ -o FILE, --output_vcf FILE\n+ output VCF to write (default: stdout)\n+ -B FILE, --bam FILE BAM or CRAM file(s), comma-separated if genotyping multiple samples\n+ -T FILE, --ref_fasta FILE\n+ Indexed reference FASTA file (recommended for reading CRAM files)\n+ -l FILE, --lib_info FILE\n+ create/read JSON file of library information\n+ -m INT, --min_aligned INT\n+ minimum number of aligned bases to consider read as evidence [20]\n+ -n INT number of reads to sample from BAM file for building insert size distribution [1000000]\n+ -q, --sum_quals add genotyping quality to existing QUAL (default: overwrite QUAL field)\n+ --max_reads INT maximum number of reads to assess at any variant (reduces processing time in high-depth regions, default: unlimited)\n+ --split_weight FLOAT weight for split reads [1]\n+ --disc_weight FLOAT weight for discordant paired-end reads [1]\n+ -w FILE, --write_alignment FILE\n+ write relevant reads to BAM file\n+ --verbose Report status updates\n+\n+ ]]>\n+ </help>\n+\n+ <citations>\n+ <citation type="doi">10.1038/nmeth.3505</citation>\n+ </citations>\n+\n+ </tool>\n'

diff -r 000000000000 -r 00cab3d2e98b test-data/out.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.vcf Wed Aug 15 15:40:54 2018 -0400

b'@@ -0,0 +1,354 @@\n+##fileformat=VCFv4.1\n+##fileDate=20180815\n+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta\n+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">\n+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">\n+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">\n+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">\n+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">\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=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">\n+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">\n+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">\n+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">\n+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">\n+##ALT=<ID=INS,Description="Insertion of novel sequence">\n+##ALT=<ID=CNV,Description="Copy number variable region">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">\n+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">\n+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">\n+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">\n+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">\n+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancest'..b'VTYPE=PE,SR;PRIN\tGT\t./.\n+3\t168738456\t206237\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-378;END=168738834;STR=+-:205;CIPOS=0,0;CIEND=0,0;EVENT=206237;SUP=205;PESUP=0;SRSUP=205;EVTYPE=SR;PRIN\tGT\t./.\n+3\t172173327\t207457\tG\t<INV>\t0.00\t.\tTOOL=LUMPY;SVTYPE=INV;SVLEN=376;END=172173703;STR=--:221;CIPOS=0,0;CIEND=0,0;EVENT=207457;SUP=221;PESUP=161;SRSUP=60;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t177294510\t209224\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-2962;END=177297472;STR=+-:261;CIPOS=0,0;CIEND=0,0;EVENT=209224;SUP=261;PESUP=177;SRSUP=84;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t177381310\t209247\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-4161;END=177385471;STR=+-:23;IMPRECISE;CIPOS=-2,58;CIEND=0,0;EVENT=209247;SUP=23;PESUP=23;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t178550130\t209676\tG\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-744;END=178550874;STR=+-:992;CIPOS=0,0;CIEND=0,0;EVENT=209676;SUP=992;PESUP=779;SRSUP=213;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t178567653\t209686\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-689;END=178568342;STR=+-:77;CIPOS=0,0;CIEND=0,0;EVENT=209686;SUP=77;PESUP=2;SRSUP=75;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t179654341\t210032\tC\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-462;END=179654803;STR=+-:1342;CIPOS=0,0;CIEND=0,0;EVENT=210032;SUP=1342;PESUP=956;SRSUP=386;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t185628683\t211946\tG\t<DUP>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DUP;SVLEN=80531;END=185709214;STR=-+:103;IMPRECISE;CIPOS=-41,1;CIEND=-2,8;EVENT=211946;SUP=103;PESUP=103;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t187732908\t212594\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1909;END=187734817;STR=+-:118;IMPRECISE;CIPOS=-2,8;CIEND=-10,1;EVENT=212594;SUP=118;PESUP=118;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t189224507\t213103\tC\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-874;END=189225381;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=213103;SUP=9;PESUP=1;SRSUP=8;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t189363422\t213158\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-7487;END=189370909;STR=+-:132;IMPRECISE;CIPOS=-1,11;CIEND=0,0;EVENT=213158;SUP=132;PESUP=132;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t190478458\t213572\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-175;END=190478633;STR=+-:151;CIPOS=0,0;CIEND=0,0;EVENT=213572;SUP=151;PESUP=10;SRSUP=141;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t192673320\t214366\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-66;END=192673386;STR=+-:108;CIPOS=0,0;CIEND=0,0;EVENT=214366;SUP=108;PESUP=1;SRSUP=107;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t192744355\t214380\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-537;END=192744892;STR=+-:229;CIPOS=0,0;CIEND=0,0;EVENT=214380;SUP=229;PESUP=217;SRSUP=12;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t192875332\t214421\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-10072;END=192885404;STR=+-:734;CIPOS=0,0;CIEND=0,0;EVENT=214421;SUP=734;PESUP=499;SRSUP=235;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t194398752\t214899\tC\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1548;END=194400300;STR=+-:293;IMPRECISE;CIPOS=-1,2;CIEND=0,0;EVENT=214899;SUP=293;PESUP=293;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t195457294\t215225\tG\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-13713;END=195471007;STR=+-:71;IMPRECISE;CIPOS=-2,9;CIEND=0,0;EVENT=215225;SUP=71;PESUP=71;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t195569217\t215275\tG\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-724;END=195569941;STR=+-:385;CIPOS=0,0;CIEND=0,0;EVENT=215275;SUP=385;PESUP=362;SRSUP=23;EVTYPE=PE,SR;PRIN\tGT\t./.\n+3\t195949296\t215374\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-2004;END=195951300;STR=+-:229;IMPRECISE;CIPOS=-1,3;CIEND=0,0;EVENT=215374;SUP=229;PESUP=229;SRSUP=0;EVTYPE=PE;PRIN\tGT\t./.\n+3\t196934573\t215670\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-4681;END=196939254;STR=+-:349;CIPOS=0,0;CIEND=0,0;EVENT=215670;SUP=349;PESUP=259;SRSUP=90;EVTYPE=PE,SR;PRIN\tGT\t./.\n+2\t84728755\t894054_1\tA\tA]15:89212842]\t0.00\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=-1,2;CIEND=0,0;MATEID=894054_2;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR;PRIN\tGT\t./.\n+15\t89212842\t894054_2\tC\tC]2:84728755]\t0.00\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=0,0;CIEND=-1,2;MATEID=894054_1;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR\tGT\t./.\n'

diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam

Binary file test-data/test1.bam has changed

diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam.bai

Binary file test-data/test1.bam.bai has changed

diff -r 000000000000 -r 00cab3d2e98b test-data/test1.bam.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.bam.json Wed Aug 15 15:40:54 2018 -0400

[

b'@@ -0,0 +1,808 @@\n+{\n+ "NA12878": {\n+ "unmapped": 10201896, \n+ "mapped": 1568288008, \n+ "bam": "/gscmnt/gc2802/halllab/sv_aggregate/MISC/realigned_BAMs/NA12878/NA12878.bam", \n+ "libraryArray": [\n+ {\n+ "library_name": "", \n+ "prevalence": 1.0, \n+ "read_length": 101, \n+ "readgroups": [\n+ "NA12878.S1"\n+ ], \n+ "histogram": {\n+ "2": 1, \n+ "4": 2, \n+ "5": 3, \n+ "6": 4, \n+ "7": 2, \n+ "8": 10, \n+ "9": 19, \n+ "10": 16, \n+ "11": 17, \n+ "12": 22, \n+ "13": 28, \n+ "14": 31, \n+ "15": 18, \n+ "16": 17, \n+ "17": 21, \n+ "18": 21, \n+ "19": 155, \n+ "20": 233, \n+ "21": 26, \n+ "22": 44, \n+ "23": 44, \n+ "24": 39, \n+ "25": 47, \n+ "26": 43, \n+ "27": 30, \n+ "28": 51, \n+ "29": 35, \n+ "30": 42, \n+ "31": 32, \n+ "32": 36, \n+ "33": 75, \n+ "34": 34, \n+ "35": 63, \n+ "36": 51, \n+ "37": 63, \n+ "38": 55, \n+ "39": 43, \n+ "40": 68, \n+ "41": 72, \n+ "42": 60, \n+ "43": 63, \n+ "44": 74, \n+ "45": 64, \n+ "46": 77, \n+ "47": 112, \n+ "48": 73, \n+ "49": 95, \n+ "50": 96, \n+ "51": 82, \n+ "52": 97, \n+ "53": 94, \n+ "54": 90, \n+ "55": 90, \n+ "56": 111, \n+ "57": 113, \n+ "58": 111, \n+ "59": 117, \n+ "60": 146, \n+ "61": 117, \n+ "62": 128, \n+ "63": 145, \n+ "64": 162, \n+ "65": 165, \n+ "66": 156, \n+ "67": 152, \n+ "68": 162, \n+ "69": 154, \n+ "70": 136, \n+ "71": 173, \n+ "72": 183, \n+ "73": 163, \n+ "74": 203, \n+ "75": 150, \n+ "76": 187, \n+ "77": 171, \n+ "78": 156, \n+ "79": 195, \n+ "80": 175, \n+ "81": 181, \n+ "82": 207, \n+ "83": 162, \n+ "84": 182, \n+ "85": 216, \n+ "86": 220, \n+ "87": 219, \n+ "88": 271, \n+ "89": 228, \n+ "90": 238, \n+ "91": 228, \n+ "92": 264, \n+ "93": 291, \n+ "94": 239, \n+ "95": 241, \n+ "96": 254, \n+ "97": 261, \n+ "98": 238, \n+ "99": 243, \n+ "100": 257, \n+ "101": 281, \n+ "102": 282, \n+ "103": 286, \n+ "104": 270, \n+ "105": 288, \n+ "106": 273, \n+ "107": 295, \n+ "108": 312, \n+ "109": 274, \n+ "110": 295, \n+ '..b' "671": 10, \n+ "672": 6, \n+ "673": 10, \n+ "674": 8, \n+ "675": 6, \n+ "676": 8, \n+ "677": 8, \n+ "678": 4, \n+ "679": 4, \n+ "680": 8, \n+ "681": 3, \n+ "682": 5, \n+ "683": 8, \n+ "684": 2, \n+ "685": 3, \n+ "686": 5, \n+ "687": 8, \n+ "688": 7, \n+ "689": 10, \n+ "690": 2, \n+ "691": 6, \n+ "692": 4, \n+ "693": 5, \n+ "694": 7, \n+ "695": 3, \n+ "696": 5, \n+ "697": 4, \n+ "698": 5, \n+ "700": 5, \n+ "701": 3, \n+ "703": 4, \n+ "705": 4, \n+ "706": 3, \n+ "707": 9, \n+ "708": 2, \n+ "710": 3, \n+ "711": 4, \n+ "712": 4, \n+ "713": 6, \n+ "714": 1, \n+ "716": 4, \n+ "717": 4, \n+ "718": 1, \n+ "719": 4, \n+ "720": 4, \n+ "721": 4, \n+ "722": 5, \n+ "723": 1, \n+ "724": 1, \n+ "726": 3, \n+ "727": 3, \n+ "729": 3, \n+ "730": 2, \n+ "731": 6, \n+ "732": 6, \n+ "735": 1, \n+ "736": 3, \n+ "737": 3, \n+ "738": 3, \n+ "739": 6, \n+ "740": 2, \n+ "741": 3, \n+ "742": 1, \n+ "743": 2, \n+ "744": 1, \n+ "745": 6, \n+ "746": 3, \n+ "747": 5, \n+ "749": 4, \n+ "750": 1, \n+ "751": 2, \n+ "752": 2, \n+ "753": 3, \n+ "754": 1, \n+ "755": 2, \n+ "756": 2, \n+ "758": 4, \n+ "759": 4, \n+ "760": 2, \n+ "762": 2, \n+ "763": 1, \n+ "764": 4, \n+ "765": 4, \n+ "766": 2, \n+ "767": 2, \n+ "768": 4, \n+ "769": 1, \n+ "770": 2, \n+ "771": 4, \n+ "772": 2, \n+ "773": 3, \n+ "774": 3, \n+ "775": 4, \n+ "776": 5, \n+ "777": 2, \n+ "778": 1, \n+ "779": 3, \n+ "780": 3, \n+ "781": 3, \n+ "782": 1, \n+ "783": 2, \n+ "784": 1, \n+ "785": 1, \n+ "786": 2, \n+ "788": 5, \n+ "789": 2, \n+ "792": 3, \n+ "3": 2, \n+ "656": 4, \n+ "699": 2, \n+ "709": 2, \n+ "733": 3, \n+ "734": 6, \n+ "761": 5, \n+ "757": 1, \n+ "702": 1, \n+ "704": 3, \n+ "715": 5, \n+ "790": 1\n+ }, \n+ "mean": 320.0287878620012, \n+ "sd": 80.21936446609676\n+ }\n+ ], \n+ "sample_name": "NA12878"\n+ }\n+}\n\\ No newline at end of file\n'

diff -r 000000000000 -r 00cab3d2e98b test-data/test1.out.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.out.vcf Wed Aug 15 15:40:54 2018 -0400

b'@@ -0,0 +1,354 @@\n+##fileformat=VCFv4.1\n+##fileDate=20180119\n+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta\n+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">\n+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">\n+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">\n+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">\n+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">\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=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">\n+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">\n+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">\n+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">\n+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">\n+##ALT=<ID=INS,Description="Insertion of novel sequence">\n+##ALT=<ID=CNV,Description="Copy number variable region">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">\n+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">\n+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">\n+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">\n+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">\n+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancest'..b'RSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:16:64:60:3:0.10:-2,-3,-7:60:3:0:0:0:60:3:0.048\n+3\t187732908\t212594\tA\t<DEL>\t224.62\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1909;END=187734817;STR=+-:118;IMPRECISE;CIPOS=-2,8;CIEND=-10,1;EVENT=212594;SUP=118;PESUP=118;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:56:42:13:224.62:-27,-4,-30:42:13:0:0:0:42:13:0.24\n+3\t189224507\t213103\tC\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-874;END=189225381;STR=+-:9;CIPOS=0,0;CIEND=0,0;EVENT=213103;SUP=9;PESUP=1;SRSUP=8;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:161:161:0:0.00:-0,-48,-160:160:0:76:0:0:84:0:0\n+3\t189363422\t213158\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-7487;END=189370909;STR=+-:132;IMPRECISE;CIPOS=-1,11;CIEND=0,0;EVENT=213158;SUP=132;PESUP=132;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:129:129:0:0.00:-0,-39,-128:128:0:58:0:0:70:0:0\n+3\t190478458\t213572\tT\t<DEL>\t1493.31\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-175;END=190478633;STR=+-:151;CIPOS=0,0;CIEND=0,0;EVENT=213572;SUP=151;PESUP=10;SRSUP=141;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:19:84:24:59:1493.31:-153,-4,-6:24:58:0:16:9:24:32:0.71\n+3\t192673320\t214366\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-66;END=192673386;STR=+-:108;CIPOS=0,0;CIEND=0,0;EVENT=214366;SUP=108;PESUP=1;SRSUP=107;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:70:70:0:0.00:-0,-21,-70:70:0:70:0:0:0:0:0\n+3\t192744355\t214380\tT\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-537;END=192744892;STR=+-:229;CIPOS=0,0;CIEND=0,0;EVENT=214380;SUP=229;PESUP=217;SRSUP=12;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:121:121:0:0.00:-0,-36,-120:120:0:55:0:0:65:0:0\n+3\t192875332\t214421\tT\t<DEL>\t824.15\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-10072;END=192885404;STR=+-:734;CIPOS=0,0;CIEND=0,0;EVENT=214421;SUP=734;PESUP=499;SRSUP=235;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:118:77:40:824.15:-86,-4,-47:76:39:39:12:2:37:24:0.34\n+3\t194398752\t214899\tC\t<DEL>\t954.46\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-1548;END=194400300;STR=+-:293;IMPRECISE;CIPOS=-1,2;CIEND=0,0;EVENT=214899;SUP=293;PESUP=293;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t1/1:51:40:5:34:954.46:-96,-6,-1:5:34:0:0:0:5:34:0.87\n+3\t195457294\t215225\tG\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-13713;END=195471007;STR=+-:71;IMPRECISE;CIPOS=-2,9;CIEND=0,0;EVENT=215225;SUP=71;PESUP=71;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0\n+3\t195569217\t215275\tG\t<DEL>\t647.37\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-724;END=195569941;STR=+-:385;CIPOS=0,0;CIEND=0,0;EVENT=215275;SUP=385;PESUP=362;SRSUP=23;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:87:55:31:647.37:-67,-3,-33:54:30:23:0:2:31:27:0.36\n+3\t195949296\t215374\tA\t<DEL>\t0.00\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-2004;END=195951300;STR=+-:229;IMPRECISE;CIPOS=-1,3;CIEND=0,0;EVENT=215374;SUP=229;PESUP=229;SRSUP=0;EVTYPE=PE;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/0:200:129:129:0:0.00:-0,-39,-128:128:0:53:0:0:75:0:0\n+3\t196934573\t215670\tA\t<DEL>\t920.21\t.\tTOOL=LUMPY;SVTYPE=DEL;SVLEN=-4681;END=196939254;STR=+-:349;CIPOS=0,0;CIEND=0,0;EVENT=215670;SUP=349;PESUP=259;SRSUP=90;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:200:106:63:42:920.21:-94,-2,-35:62:41:27:9:3:35:28:0.4\n+2\t84728755\t894054_1\tA\tA]15:89212842]\t65.75\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=-1,2;CIEND=0,0;MATEID=894054_2;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR;PRIN\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16\n+15\t89212842\t894054_2\tC\tC]2:84728755]\t65.75\t.\tTOOL=LUMPY;SVTYPE=BND;STR=++:74;IMPRECISE;CIPOS=0,0;CIEND=-1,2;MATEID=894054_1;EVENT=894054;SUP=74;PESUP=73;SRSUP=1;EVTYPE=PE,SR\tGT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB\t0/1:65:39:32:6:65.75:-12,-5,-26:32:6:0:0:0:32:6:0.16\n'

diff -r 000000000000 -r 00cab3d2e98b test-data/test1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.vcf Wed Aug 15 15:40:54 2018 -0400

b'@@ -0,0 +1,344 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140901\n+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta\n+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">\n+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">\n+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">\n+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">\n+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">\n+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">\n+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">\n+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">\n+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">\n+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">\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=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">\n+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">\n+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">\n+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">\n+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">\n+##ALT=<ID=DEL,Description="Deletion">\n+##ALT=<ID=DUP,Description="Duplication">\n+##ALT=<ID=INV,Description="Inversion">\n+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">\n+##ALT=<ID=INS,Description="Insertion of novel sequence">\n+##ALT=<ID=CNV,Description="Copy number variable region">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">\n+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">\n+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">\n+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">\n+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">\n+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">\n+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">\n+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">\n+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of 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