From 85bc9d3e91a85da51a42212421b7f569fb025416 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 18 Nov 2009 23:33:27 +0000
Subject: [PATCH] (Hopefully) temporary hack: load contig information by contig
 name rather than contig id to avoid off-by-one errors.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/iterators/LocusIteratorByState.java              | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
index 402d3fd7d..1976ab819 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
@@ -92,7 +92,7 @@ public class LocusIteratorByState extends LocusIterator {
         public int getGenomePosition() { return read.getAlignmentStart() + getGenomeOffset(); }
 
         public GenomeLoc getLocation() {
-            return GenomeLocParser.createGenomeLoc(read.getReferenceIndex(), getGenomePosition());
+            return GenomeLocParser.createGenomeLoc(read.getReferenceName(), getGenomePosition());
         }
 
         //private CigarElement getCurElement() { return curElement; }