# HG changeset patch
# User hepcat72
# Date 1539366480 14400
# Node ID 2ba5317566c05c4cd4dac7e6f1c03aa5550389eb
# Parent  00cab3d2e98b8e4b202e120e3fe30e6008361312
planemo upload commit c214e5fa219f8d3593ac8aad9e15f9eeba5320f5

diff -r 00cab3d2e98b -r 2ba5317566c0 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Oct 12 13:48:00 2018 -0400
@@ -0,0 +1,17 @@
+# svtyper galaxy tool wrapper
+
+## About
+
+This is a galaxy tool wrapper written for svtyper, which can be found here:
+
+https://github.com/hall-lab/svtyper
+
+Issues with the wrapper can be submitted here in this repo.  Issues with svtyper should be submitted to the svtyper developers at:
+
+https://github.com/hall-lab/svtyper/issues
+
+## Install
+
+This wrapper is available for install via the main galaxy tool shed:
+
+https://toolshed.g2.bx.psu.edu
\ No newline at end of file
diff -r 00cab3d2e98b -r 2ba5317566c0 svtyper.xml
--- a/svtyper.xml	Wed Aug 15 15:40:54 2018 -0400
+++ b/svtyper.xml	Fri Oct 12 13:48:00 2018 -0400
@@ -103,6 +103,7 @@
         <param name="libin"
                label="Library json file"
                argument="--lib_info"
+               optional="true"
 
                type="data"
                format="json"
@@ -201,6 +202,13 @@
             <output name="vcfout" file="test1.out.vcf"
                     compare="diff" lines_diff="2" />
         </test>
+        <test>
+            <!-- Test no input json lib file -->
+            <param name="vcf" value="test1.vcf"/>
+            <param name="alignment_files" value="test1.bam"/>
+            <output name="vcfout" file="test2.out.vcf"
+                    compare="diff" lines_diff="2" />
+        </test>
     </tests>
     <help>
         <![CDATA[
diff -r 00cab3d2e98b -r 2ba5317566c0 test-data/test2.out.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.out.vcf	Fri Oct 12 13:48:00 2018 -0400
@@ -0,0 +1,354 @@
+##fileformat=VCFv4.1
+##fileDate=20181012
+##reference=/shared/genomes/b37/full/human_g1k_v37.fasta
+##INFO=<ID=TOOL,Number=1,Type=String,Description="Tool used to generate variant call">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=STR,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=SUP,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
+##INFO=<ID=PESUP,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
+##INFO=<ID=SRSUP,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
+##INFO=<ID=EVTYPE,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
+##INFO=<ID=PRIN,Number=0,Type=Flag,Description="Indicates variant as the principal variant in a BEDPE pair">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
+##ALT=<ID=INV,Description="Inversion">
+##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
+##ALT=<ID=INS,Description="Insertion of novel sequence">
+##ALT=<ID=CNV,Description="Copy number variable region">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=SUP,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
+##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
+##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood form imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
+##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
+##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
+##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
+##contig=<ID=1,length=249250621>
+##contig=<ID=2,length=243199373>
+##contig=<ID=3,length=198022430>
+##contig=<ID=4,length=191154276>
+##contig=<ID=5,length=180915260>
+##contig=<ID=6,length=171115067>
+##contig=<ID=7,length=159138663>
+##contig=<ID=8,length=146364022>
+##contig=<ID=9,length=141213431>
+##contig=<ID=10,length=135534747>
+##contig=<ID=11,length=135006516>
+##contig=<ID=12,length=133851895>
+##contig=<ID=13,length=115169878>
+##contig=<ID=14,length=107349540>
+##contig=<ID=15,length=102531392>
+##contig=<ID=16,length=90354753>
+##contig=<ID=17,length=81195210>
+##contig=<ID=18,length=78077248>
+##contig=<ID=19,length=59128983>
+##contig=<ID=20,length=63025520>
+##contig=<ID=21,length=48129895>
+##contig=<ID=22,length=51304566>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##contig=<ID=MT,length=16569>
+##contig=<ID=GL000207.1,length=4262>
+##contig=<ID=GL000226.1,length=15008>
+##contig=<ID=GL000229.1,length=19913>
+##contig=<ID=GL000231.1,length=27386>
+##contig=<ID=GL000210.1,length=27682>
+##contig=<ID=GL000239.1,length=33824>
+##contig=<ID=GL000235.1,length=34474>
+##contig=<ID=GL000201.1,length=36148>
+##contig=<ID=GL000247.1,length=36422>
+##contig=<ID=GL000245.1,length=36651>
+##contig=<ID=GL000197.1,length=37175>
+##contig=<ID=GL000203.1,length=37498>
+##contig=<ID=GL000246.1,length=38154>
+##contig=<ID=GL000249.1,length=38502>
+##contig=<ID=GL000196.1,length=38914>
+##contig=<ID=GL000248.1,length=39786>
+##contig=<ID=GL000244.1,length=39929>
+##contig=<ID=GL000238.1,length=39939>
+##contig=<ID=GL000202.1,length=40103>
+##contig=<ID=GL000234.1,length=40531>
+##contig=<ID=GL000232.1,length=40652>
+##contig=<ID=GL000206.1,length=41001>
+##contig=<ID=GL000240.1,length=41933>
+##contig=<ID=GL000236.1,length=41934>
+##contig=<ID=GL000241.1,length=42152>
+##contig=<ID=GL000243.1,length=43341>
+##contig=<ID=GL000242.1,length=43523>
+##contig=<ID=GL000230.1,length=43691>
+##contig=<ID=GL000237.1,length=45867>
+##contig=<ID=GL000233.1,length=45941>
+##contig=<ID=GL000204.1,length=81310>
+##contig=<ID=GL000198.1,length=90085>
+##contig=<ID=GL000208.1,length=92689>
+##contig=<ID=GL000191.1,length=106433>
+##contig=<ID=GL000227.1,length=128374>
+##contig=<ID=GL000228.1,length=129120>
+##contig=<ID=GL000214.1,length=137718>
+##contig=<ID=GL000221.1,length=155397>
+##contig=<ID=GL000209.1,length=159169>
+##contig=<ID=GL000218.1,length=161147>
+##contig=<ID=GL000220.1,length=161802>
+##contig=<ID=GL000213.1,length=164239>
+##contig=<ID=GL000211.1,length=166566>
+##contig=<ID=GL000199.1,length=169874>
+##contig=<ID=GL000217.1,length=172149>
+##contig=<ID=GL000216.1,length=172294>
+##contig=<ID=GL000215.1,length=172545>
+##contig=<ID=GL000205.1,length=174588>
+##contig=<ID=GL000219.1,length=179198>
+##contig=<ID=GL000224.1,length=179693>
+##contig=<ID=GL000223.1,length=180455>
+##contig=<ID=GL000195.1,length=182896>
+##contig=<ID=GL000212.1,length=186858>
+##contig=<ID=GL000222.1,length=186861>
+##contig=<ID=GL000200.1,length=187035>
+##contig=<ID=GL000193.1,length=189789>
+##contig=<ID=GL000194.1,length=191469>
+##contig=<ID=GL000225.1,length=211173>
+##contig=<ID=GL000192.1,length=547496>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
+2	2798774	72354	C	<DEL>	1059.24	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-467;END=2799241;STR=+-:840;CIPOS=0,0;CIEND=0,0;EVENT=72354;SUP=840;PESUP=608;SRSUP=232;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:7:58:16:42:1059.24:-109,-3,-4:16:41:0:15:4:16:21:0.72
+2	3732805	72623	C	<DEL>	755.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5222;END=3738027;STR=+-:212;CIPOS=0,0;CIEND=0,0;EVENT=72623;SUP=212;PESUP=192;SRSUP=20;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:81:46:34:755.39:-77,-1,-24:45:33:21:2:4:24:26:0.42
+2	6400508	73459	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1684;END=6402192;STR=+-:38;CIPOS=0,0;CIEND=0,0;EVENT=73459;SUP=38;PESUP=27;SRSUP=11;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:65:0:0:61:0:0
+2	14704171	76210	G	<DEL>	1013.14	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5944;END=14710115;STR=+-:293;CIPOS=0,0;CIEND=0,0;EVENT=76210;SUP=293;PESUP=218;SRSUP=75;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:115:68:46:1013.14:-103,-2,-37:67:45:31:11:2:36:31:0.4
+2	16271643	76851	G	<DEL>	221.88	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2219;END=16273862;STR=+-:196;IMPRECISE;CIPOS=-1,6;CIEND=-5,1;EVENT=76851;SUP=196;PESUP=196;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:25:16:7:9:221.88:-23,-1,-3:7:9:0:0:0:7:9:0.56
+2	18906149	76667	T	<DEL>	884.01	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1198;END=18907347;STR=+-:313;CIPOS=0,0;CIEND=0,0;EVENT=76667;SUP=313;PESUP=226;SRSUP=87;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:138:93:44:884.01:-93,-5,-58:92:43:39:13:1:53:28:0.32
+2	28661666	80866	C	<DEL>	224.74	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-51;END=28661717;STR=+-:202;CIPOS=0,0;CIEND=0,0;EVENT=80866;SUP=202;PESUP=0;SRSUP=202;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:139:36:24:11:224.74:-24,-2,-16:24:11:24:11:0:0:0:0.31
+2	30934974	81625	C	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-120;END=30935094;STR=+-:8;CIPOS=0,0;CIEND=0,0;EVENT=81625;SUP=8;PESUP=1;SRSUP=7;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:186:62:62:0:0.00:-0,-19,-62:62:0:62:0:0:0:0:0
+2	33224462	82677	A	<DEL>	749.25	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2829;END=33227291;STR=+-:357;CIPOS=0,0;CIEND=0,0;EVENT=82677;SUP=357;PESUP=263;SRSUP=94;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:102:66:36:749.25:-78,-3,-40:65:35:33:11:2:32:21:0.35
+2	34523656	83127	G	<DEL>	1277.09	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-2062;END=34525718;STR=+-:1031;CIPOS=0,0;CIEND=0,0;EVENT=83127;SUP=1031;PESUP=719;SRSUP=312;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:117:61:55:1277.09:-129,-1,-29:60:54:28:17:2:32:34:0.47
+2	34965729	83280	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1539;END=34967268;STR=+-:86;CIPOS=0,0;CIEND=0,0;EVENT=83280;SUP=86;PESUP=61;SRSUP=25;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:127:127:0:0.00:-0,-38,-126:126:0:61:0:0:65:0:0
+2	35007246	83301	G	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-578;END=35007824;STR=+-:16;CIPOS=0,0;CIEND=0,0;EVENT=83301;SUP=16;PESUP=0;SRSUP=16;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:147:147:0:0.00:-0,-44,-146:146:0:69:0:0:77:0:0
+2	35772266	83555	A	<DEL>	305.71	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-52;END=35772318;STR=+-:109;CIPOS=0,0;CIEND=0,0;EVENT=83555;SUP=109;PESUP=1;SRSUP=108;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:132:39:24:14:305.71:-32,-1,-15:24:14:24:14:0:0:0:0.37
+2	40446947	85115	T	<DEL>	155.73	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-125;END=40447072;STR=+-:100;CIPOS=0,0;CIEND=0,0;EVENT=85115;SUP=100;PESUP=0;SRSUP=100;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:155:39:29:9:155.73:-19,-3,-21:29:9:29:9:0:0:0:0.24
+2	41238369	85376	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-11934;END=41250303;STR=+-:41;CIPOS=0,0;CIEND=0,0;EVENT=85376;SUP=41;PESUP=29;SRSUP=12;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:135:135:0:0.00:-0,-40,-134:134:0:60:0:0:74:0:0
+2	41775966	85577	T	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-5316;END=41781282;STR=+-:287;CIPOS=0,0;CIEND=0,0;EVENT=85577;SUP=287;PESUP=227;SRSUP=60;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:158:158:0:0.00:-0,-47,-157:157:0:80:0:0:77:0:0
+2	42346259	85762	C	<DEL>	512.36	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1086;END=42347345;STR=+-:204;IMPRECISE;CIPOS=-1,13;CIEND=0,0;EVENT=85762;SUP=204;PESUP=204;SRSUP=0;EVTYPE=PE;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:92:64:27:512.36:-56,-4,-42:63:26:31:3:2:32:21:0.29
+2	43854262	86202	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-217;END=43854479;STR=+-:57;CIPOS=0,0;CIEND=0,0;EVENT=86202;SUP=57;PESUP=3;SRSUP=54;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:72:72:0:0.00:-0,-22,-72:72:0:72:0:0:0:0:0
+2	48851192	87923	A	<DEL>	0.00	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-6759;END=48857951;STR=+-:521;CIPOS=0,0;CIEND=0,0;EVENT=87923;SUP=521;PESUP=381;SRSUP=140;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/0:200:144:144:0:0.00:-0,-43,-143:143:0:70:0:0:73:0:0
+2	48990526	87970	T	<DEL>	419.36	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-637;END=48991163;STR=+-:458;CIPOS=0,0;CIEND=0,0;EVENT=87970;SUP=458;PESUP=314;SRSUP=144;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:93:68:24:419.36:-48,-6,-47:67:23:30:6:3:37:13:0.26
+2	49561484	88177	G	<DEL>	620.39	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-141;END=49561625;STR=+-:163;CIPOS=0,0;CIEND=0,0;EVENT=88177;SUP=163;PESUP=3;SRSUP=160;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:53:21:0:21:620.39:-63,-6,-1:0:21:0:21:0:0:0:1
+2	51926587	88990	A	<DEL>	722.26	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-1179;END=51927766;STR=+-:383;CIPOS=0,0;CIEND=0,0;EVENT=88990;SUP=383;PESUP=273;SRSUP=110;EVTYPE=PE,SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:102:66:35:722.26:-75,-3,-40:65:34:25:7:3:40:23:0.34
+2	51973823	89011	A	<DEL>	620.19	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-416;END=51974239;STR=+-:76;CIPOS=0,0;CIEND=0,0;EVENT=89011;SUP=76;PESUP=0;SRSUP=76;EVTYPE=SR;PRIN	GT:GQ:DP:RO:AO:SQ:GL:QR:QA:RS:AS:ASC:RP:AP:AB	0/1:200:115:82:33:620.19:-68,-6,-54:81:32:31:6:7:50:18:0.28
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