From d9202f2764d67a7e84a3643459e0bc9b9002d8e7 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 21 Mar 2011 13:46:55 +0000
Subject: [PATCH] Don't try to create a GenomeLoc from an unmapped read

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5480 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/ConstrainedMateFixingManager.java    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index 9fae0c132..0c43a063f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -183,8 +183,9 @@ public class ConstrainedMateFixingManager {
                 writeRead(waitingReads.remove());
             }
 
-            lastLocFlushed = genomeLocParser.createGenomeLoc(waitingReads.peek());
-            writeRead(waitingReads.remove());
+            SAMRecord lastRead = waitingReads.remove();
+            lastLocFlushed = (lastRead.getReferenceIndex() == -1) ? null : genomeLocParser.createGenomeLoc(lastRead);
+            writeRead(lastRead);
 
             if ( !tooManyReads )
                 forMateMatching.clear();