From a640bd2d79d1914ef93260f4c595518b314c592b Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 22 Feb 2010 19:55:46 +0000
Subject: [PATCH] ignore uninteresting extended events

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2866 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java    | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index 10466f9c5..6d871af3f 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -114,9 +114,14 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
                 hasPointEvent = true;
         }
 
+        // return null if no event occurred
         if ( !hasIndel && !hasPointEvent )
             return null;
 
+        // return null if we didn't find any usable reads associated with the event
+        if ( furthestStopPos == -1 )
+            return null;
+
         GenomeLoc eventLoc = context.getLocation();
         if ( hasInsertion )
             eventLoc =  GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), eventLoc.getStart()+1);