From d35a542bb9ab5e3df1a5bf55c09ce9cee738748e Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Apr 2009 12:53:07 +0000
Subject: [PATCH] * fixed bug where the merged header was not being set on the
 read (although the read group was)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/MergingSamRecordIterator2.java          | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index f560f9acb..b308a6db6 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -134,6 +134,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
             record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
         }
 
+        record.setHeader(samHeaderMerger.getMergedHeader());
         //System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());
         //System.out.printf("PEEK = %s %s %d%n", this.pq.peek().peek().getReadName(), this.pq.peek().peek().getReferenceName(), this.pq.peek().peek().getAlignmentStart());
         return record;