From 585a45b7a3d145fbb1ed135c2a78d03bd6e8bf7c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 23 Oct 2011 16:36:48 -0400
Subject: [PATCH] Bug fix for ClipReadsWalker when stats output isn't provided

-- See http://getsatisfaction.com/gsa/topics/clipreadswalker?utm_content=topic_link&utm_medium=email&utm_source=reply_notification
---
 .../org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index bb65d9b09..6989f45b2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -475,7 +475,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipperWithD
     }
 
     public void onTraversalDone(ClippingData data) {
-        out.printf(data.toString());
+        if ( out != null )
+            out.printf(data.toString());
     }
 
     // --------------------------------------------------------------------------------------------------------------