From 2520889cb35d09acf8313868c542bdfd98b9ae80 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Feb 2010 21:42:36 +0000
Subject: [PATCH] Check for bad intervals and don't emit them

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 c2838f115..10466f9c5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -214,7 +214,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
         }
 
         public boolean isReportableEvent() {
-            return eventStartPos >= 0 && eventStopPos >= 0 && eventStopPos - eventStartPos < maxIntervalSize;
+            return GenomeLocParser.validGenomeLoc(loc.getContig(), eventStartPos, eventStopPos) && eventStopPos >= 0 && eventStopPos - eventStartPos < maxIntervalSize;
         }
 
         public String toString() {