diff test-data/result-2.vcf @ 10:8711df965d4b draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223

--- a/test-data/result-2.vcf	Wed Apr 05 15:56:13 2023 +0000
+++ b/test-data/result-2.vcf	Wed Jan 24 19:26:57 2024 +0000
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20230405
+##fileDate=20240124
 ##reference=reference.fa
 ##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">
@@ -44,16 +44,16 @@
 ##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=chrI,length=15072434>
+##contig=<ID=chrI_sub,length=100000>
 ##smoove_version=0.2.8
-##smoove_count_stats=celegans-1:2869,2691,202,330
-##smoove_count_stats=celegans-2:2531,2421,156,296
+##smoove_count_stats=RG1:0,638,0,598
+##smoove_count_stats=RG2:0,466,0,448
 ##source=LUMPY
-##bcftools_annotateVersion=1.16+htslib-1.17
-##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Apr  5 13:40:08 2023
+##bcftools_annotateVersion=1.17+htslib-1.17
+##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Jan 24 19:27:21 2024
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##bcftools_viewVersion=1.16+htslib-1.17
-##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Apr  5 13:40:08 2023
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	celegans-1	celegans-2
-chrI	10416569	1	N	<DUP>	170.7	.	SVTYPE=DUP;SVLEN=981;END=10417550;STRANDS=-+:4;IMPRECISE;CIPOS=-769,29;CIEND=-30,636;CIPOS95=-165,8;CIEND95=-9,128;SU=4;PE=4;SR=0;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:16:130.28:-15,-4,-2:14:4:9:4:9:0:0:0:4:9:0.69	1/1:3:40.43:-4,-1,-1:7:4:3:4:3:0:0:0:4:3:0.43
+##bcftools_viewVersion=1.17+htslib-1.17
+##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:27:21 2024
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	RG1	RG2
+chrI_sub	50007	1	N	<DUP>	103.66	.	SVTYPE=DUP;SVLEN=1148;END=51155;STRANDS=-+:5;IMPRECISE;CIPOS=0,22;CIEND=-30,331;CIPOS95=0,10;CIEND95=-10,82;SU=5;PE=5;SR=0;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:10:74.81:-9,-3,-2:7:1:5:1:5:0:0:0:1:5:0.83	1/1:2:28.84:-3,-1,-1:5:2:2:2:2:0:0:0:2:2:0.5