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Commit 31a7e23d authored by Sander Bollen's avatar Sander Bollen
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small refactor: method name correction

parent a1605bf2
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......@@ -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
......
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