From 75bd0129e707c0844c60b9e457ceffc3f572541c Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Feb 2011 19:16:20 +0000
Subject: [PATCH] quick bug fix.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5296 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
index 0014b91fa..fd2d53827 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@@ -116,7 +116,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @return the SAMFileWriter, so that the next reduce can emit to the same source
      */
     public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
-        out.addAlignment(read);
+        output.addAlignment(read);
         return output;
     }