From f5eae98af2e147af45d8848f48c493fb3fd089e1 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 May 2009 18:40:55 +0000
Subject: [PATCH] Fixed a bug where we could ask for a read when there were
 none in the pool (that's a bad thing).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 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 ddc111257..a99fd8e79 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
@@ -150,7 +150,11 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         if (!initialized) {
             lazyInitialization();
         }
+
         final ComparableSamRecordIterator iterator = this.pq.poll();
+        if (iterator == null) {
+            return null;
+        }
         final SAMRecord record = iterator.next();
         addIfNotEmpty(iterator);