From 5d4bbf41fbe1eea5dba3773a6b4fd706bfe6fdb7 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Mar 2011 04:52:55 +0000
Subject: [PATCH] Behave intelligently in the deepest levels of GATK record
 filtration when we find a read flagged as 'mapped' in the unmapped region at
 the end of the file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5365 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/SAMDataSource.java    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
index 57a01c20a..5e78e3e0e 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
@@ -974,11 +974,11 @@ public class SAMDataSource {
                     }
                 }
                 else {
-                    // Unmapped read filter; just check getReadUnmappedFlag().
-                    if(!candidateRead.getReadUnmappedFlag())
-                        continue;
-                    nextRead = candidateRead;
-                    break;
+                    // Found an unmapped read.  We're done.
+                    if(candidateRead.getReadUnmappedFlag()) {
+                        nextRead = candidateRead;
+                        break;
+                    }
                 }
 
                 // No more reads available.  Stop the search.