From c5f105d0502a7cec5ca906527e308bf115cc752f Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 19 Oct 2010 01:20:12 +0000
Subject: [PATCH] Fix boneheaded mistake in the new interval filtering code I
 added on Sunday. Sorry everyone.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4521 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/datasources/simpleDataSources/SAMDataSource.java  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index 4e567ed54..1c063230d 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -823,9 +823,12 @@ public class SAMDataSource implements SimpleDataSource {
                     }
                 }
 
+                // No more reads available.  Stop the search.
+                if(!iterator.hasNext())
+                    break;
+
                 // No reasonable read found; advance the iterator.
-                if(iterator.hasNext())
-                    candidateRead = iterator.next();                
+                candidateRead = iterator.next();
             }
         }
     }