From 152f65b362d2f62202d13e94d9560a8a25d1445d Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 4 Feb 2010 19:48:12 +0000
Subject: [PATCH] Do not die in --cycleOnly mode when the lane is not paired
 end, just count all single end basequals into the first column and leave the
 second column filled with 0s

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2778 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffprojects/walkers/QualityScoreByStrandWalker.java  | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
index bb9e933ae..8ecd7b5b6 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
@@ -82,7 +82,11 @@ public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,Stran
         if ( ! useCycle ) {
             counts.updateLocus( (int) e.getQual(), ! e.getRead().getReadNegativeStrandFlag() );
         } else {
-            counts.updateLocus( (int) e.getQual(), ! e.getRead().getFirstOfPairFlag() );
+            if ( e.getRead().getReadPairedFlag() ) {
+                counts.updateLocus( (int) e.getQual(), e.getRead().getFirstOfPairFlag() );
+            } else {
+                counts.updateLocus( (int) e.getQual(), true );
+            }
         }
     }