Commit c3321a66 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed position check

parent 069db857
......@@ -45,9 +45,11 @@ object ValidateVcf extends ToolCommand {
s"contig in vcf file is not on reference: ${contig}")
val start = record.getStart
val end = record.getEnd
require(regions.chrRecords(contig).exists(_.overlapWith(BedRecord("contig", start, start))),
val contigStart = regions.chrRecords(contig).head.start
val contigEnd = regions.chrRecords(contig).head.end
require(start >= contigStart && start <= contigEnd,
s"Position does not exist on reference: ${contig}:$start")
if (end != start) require(regions.chrRecords(contig).exists(_.overlapWith(BedRecord("contig", end, end))),
if (end != start) require(end >= contigStart && end <= contigEnd,
s"Position does not exist on reference: ${contig}:$end")
require(start <= end, "End is higher then Start, this should not be possible")
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