From a9df0f227c5f0d224834b7a0e24d42b0a3974fc2 Mon Sep 17 00:00:00 2001 From: Wai Yi Leung <w.y.leung@lumc.nl> Date: Fri, 13 May 2016 15:13:18 +0200 Subject: [PATCH] Test output file needed --- .../clever/expectedresult.clever.vcf | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/expectedresult.clever.vcf diff --git a/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/expectedresult.clever.vcf b/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/expectedresult.clever.vcf new file mode 100644 index 000000000..5623fc963 --- /dev/null +++ b/biopet-extensions/src/test/resources/nl/lumc/sasc/biopet/extensions/clever/expectedresult.clever.vcf @@ -0,0 +1,43 @@ +##fileformat=VCFv4.2 +##fileDate=20150730 +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation"> +##INFO=<ID=SVEND,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##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=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=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=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file"> +##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY"> +##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY"> +##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation"> +##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR"> +##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP"> +##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends"> +##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend"> +##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend"> +##INFO=<ID=BPWINDOW,Number=2,Type=Integer,Description="Window of breakpoints"> +##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend"> +##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency"> +##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend"> +##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency"> +##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment"> +##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency"> +##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 for 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=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testsample +chrM 352 L170961 N <DEL> . PASS BPWINDOW=353,16175;CILEN=15817,15829;IMPRECISE;SVLEN=-15823;SVTYPE=DEL GT:DP 1/.:76 -- GitLab