diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala index 2797ffc2de25d6045f7717947149cd3900437ced..919316c2ba04a3c69005a7fa1a1a5464d3629c3a 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala @@ -116,7 +116,7 @@ object CheckAllelesVcfInBam extends ToolCommand { } val counts = for (samRecord <- bamIter if !filterRead(samRecord)) { - checkAlles(samRecord, vcfRecord) match { + checkAlleles(samRecord, vcfRecord) match { case Some(a) => if (countReports(sample).aCounts.contains(a)) countReports(sample).aCounts(a) += 1 else countReports(sample).aCounts += (a -> 1) case _ => countReports(sample).notFound += 1 @@ -142,7 +142,7 @@ object CheckAllelesVcfInBam extends ToolCommand { writer.close() } - def checkAlles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String] = { + def checkAlleles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String] = { val readStartPos = List.range(0, samRecord.getReadBases.length) .find(x => samRecord.getReferencePositionAtReadPosition(x + 1) == vcfRecord.getStart) getOrElse { return None } val readBases = samRecord.getReadBases