fix

fulcrumgenomics · Mar 10, 2022 · 5ebd61f · 5ebd61f
1 parent 8468d64
commit 5ebd61f
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala b/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala
@@ -93,15 +93,15 @@ class OverlappingBasesConsensusCaller {
         r2LastReadPos = r2Head.read
         r2Iter.next()
       }
-      if (r1Head.ref == r2Head.ref) { // matched reference bases, so consensus call
+      else { // matched reference bases, so consensus call
         // add read bases from insertions
         r1BasesBuilder.addAll(r1Bases.slice(from=r1LastReadPos + 1, until=r1Head.read))
         r1QualsBuilder.addAll(r1Quals.slice(from=r1LastReadPos + 1, until=r1Head.read))
         r2BasesBuilder.addAll(r2Bases.slice(from=r2LastReadPos + 1, until=r2Head.read))
         r2QualsBuilder.addAll(r2Quals.slice(from=r2LastReadPos + 1, until=r2Head.read))
 
         r1OverlappingBases += 1
-        r2OverlappingBases += 2
+        r2OverlappingBases += 1
 
         // consensus call current
         val (base, qual) = consensusCall(