From 4edb33788b748ddf798745b85d2ed505500bd055 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 1 Jun 2009 16:53:56 +0000
Subject: [PATCH] added a fix for a bug Andrew found

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@869 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/MergingSamRecordIterator2.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index 0f2497cba..187df3c74 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -184,7 +184,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         }
 
         record.setHeader(samHeaderMerger.getMergedHeader());
-        if (this.samHeaderMerger.hasMergedSequenceDictionary()) {
+        if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() > 0) {
             record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
         }