diff --git a/test/intersect/bug223_f.vcf b/test/intersect/bug223_f.vcf new file mode 100644 index 0000000000000000000000000000000000000000..ba98303668c1691b5d0080e531aea3d399d94f53 --- /dev/null +++ b/test/intersect/bug223_f.vcf @@ -0,0 +1,3 @@ +##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 diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh index 76e211ecc975a2a763ee0008b4a4ad19684a192c..7e8cc32df9db5b40fbe3e7462a6483e702f91655 100644 --- a/test/intersect/test-intersect.sh +++ b/test/intersect/test-intersect.sh @@ -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