From a3f59325016b9ffb78f71941aa9fd54bb9e4b3d6 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 26 Nov 2012 11:12:27 -0500
Subject: [PATCH] Fixed null pointer exception in Integration Tests

When running Utils.setupWriter with NO_PG_TAG set, the writer was attempting to create a program record with the null pointer. Fixed.
---
 public/java/src/org/broadinstitute/sting/utils/Utils.java | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java
index b780d0966..544030f73 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -701,11 +701,13 @@ public class Utils {
         List<SAMProgramRecord> oldRecords = header.getProgramRecords();
         List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
         for ( SAMProgramRecord record : oldRecords )
-            if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS )
+            if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())) || KEEP_ALL_PG_RECORDS )
                 newRecords.add(record);
 
-        newRecords.add(programRecord);
-        header.setProgramRecords(newRecords);
+        if (programRecord != null) {
+            newRecords.add(programRecord);
+            header.setProgramRecords(newRecords);
+        }
         return header;
     }