From 035d4170aa8236d8d560fc830ea0fe693d1872dd Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Mar 2010 18:49:26 +0000
Subject: [PATCH] fix bug in read clipper: output bam can be null, so check for
 it.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index 614a08d52..80221be41 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -123,7 +123,8 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
             }
         }
 
-        outputBam.setPresorted(clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES);
+        if (outputBam != null)
+            outputBam.setPresorted(clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES);
     }
 
     /**