From d1c5e986d5519e6f39f4875e7dca4bfa31ffdf3f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 6 Apr 2009 04:58:22 +0000
Subject: [PATCH] Another check to deal with bad reads (BWA output throws bad
 exceptions)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@298 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 21326424f..7cb725508 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -130,7 +130,10 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     }
 
     public static GenomeLoc genomicLocationOf(final SAMRecord read) {
-        return new GenomeLoc(read.getReferenceName(), read.getAlignmentStart(), read.getAlignmentEnd());
+        String contig = read.getReferenceName();
+        if (read.getReadUnmappedFlag())
+            contig = null;
+        return new GenomeLoc(contig, read.getAlignmentStart(), read.getAlignmentEnd());
     }
 
     // --------------------------------------------------------------------------------------------------------------