From cebfd018578be6875f4274c67d9eda2539ff1656 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Dec 2010 14:49:24 +0000
Subject: [PATCH] Properly output .bed

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4905 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/CreateTriggerTrack.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java
index e836b071c..97a69deb7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java
@@ -47,7 +47,7 @@ public class CreateTriggerTrack extends RodWalker<Integer, Integer> {
 
         Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
         if ( VCs.size() > 0 )
-            writer.println(context.getLocation().getContig() + "\t" + context.getLocation().getStart() + "\t" + context.getLocation().getStart());
+            writer.println(context.getLocation().getContig() + "\t" + (context.getLocation().getStart()-1) + "\t" + context.getLocation().getStart());
 
         return 0;
     }