From ba2a3d8a586e5f3a88a2aa39012ec3a2524cf3a4 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 12 Aug 2009 20:17:35 +0000
Subject: [PATCH] Reverse qualities when read seq. is reverse complemented

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1417 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/fasta/BamToFastqWalker.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
index 778c055c1..aa7406ae7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/BamToFastqWalker.java
@@ -23,7 +23,7 @@ public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
         } else {
             out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
             out.println("+");
-            out.println(BaseUtils.simpleReverseComplement(read.getBaseQualityString()));
+            out.println(BaseUtils.reverse(read.getBaseQualityString()));
         }
 
         return 1;