Commit 9724fbbe authored by Neil Kindlon's avatar Neil Kindlon
Browse files

Added extra unit test for vcf svlen - single # at end of line

parent ca31d1f2
##fileformat=VCFv4.1
chr1 1 a G <DEL> 70.90 . TOOL=LUMPY;SVTYPE=DEL;SVLEN=-389,-4611;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||
chr1 4 a G <DEL> 70.90 . TOOL=LUMPY;SVTYPE=DEL;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||;SVLEN=-10
\ No newline at end of file
......@@ -610,6 +610,20 @@ $BT intersect -a bug223_e.vcf -b bug223_e.vcf | cut -f1-6 > obs
check exp obs
rm exp obs
##################################################################
# see that SVLEN in VCF files can handle single numbers,
# at end of line, followed by null
##################################################################
echo " intersect.t50...\c"
echo \
"chr1 1 a G <DEL> 70.90
chr1 1 a G <DEL> 70.90
chr1 4 a G <DEL> 70.90
chr1 4 a G <DEL> 70.90" > exp
$BT intersect -a bug223_f.vcf -b bug223_f.vcf | cut -f1-6 > obs
check exp obs
rm exp obs
cd multi_intersect
......
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