From 31a7e23dc9e3b0f69d373e2f348ff7e887370888 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 26 Aug 2015 18:08:53 +0200
Subject: [PATCH] small refactor: method name correction
---
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
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 2797ffc2d..919316c2b 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
--
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