From 5ebd61f7aba69449c9c7d47bf55e3912148758f7 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Thu, 10 Mar 2022 01:53:43 -0700
Subject: [PATCH] fix

---
 .../personal/nhomer/OverlappingBasesConsensusCaller.scala     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala b/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala
index a431d73e3..ade3454be 100644
--- a/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala
+++ b/src/main/scala/com/fulcrumgenomics/personal/nhomer/OverlappingBasesConsensusCaller.scala
@@ -93,7 +93,7 @@ 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))
@@ -101,7 +101,7 @@ class OverlappingBasesConsensusCaller {
         r2QualsBuilder.addAll(r2Quals.slice(from=r2LastReadPos + 1, until=r2Head.read))
 
         r1OverlappingBases += 1
-        r2OverlappingBases += 2
+        r2OverlappingBases += 1
 
         // consensus call current
         val (base, qual) = consensusCall(