From 0cf90b6f8a1e4c0d1ee30a8a223253621cd73884 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 28 May 2009 21:48:35 +0000
Subject: [PATCH] Tie into sequence merging code in the latest version of
 picard.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@851 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/MergingSamRecordIterator2.java       | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 0e9d4cafc..0f2497cba 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -184,6 +184,10 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         }
 
         record.setHeader(samHeaderMerger.getMergedHeader());
+        if (this.samHeaderMerger.hasMergedSequenceDictionary()) {
+            record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
+        }
+        
         //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());