From 998763950caa353a1a655356e2af50e6b726db16 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Apr 2009 19:08:16 +0000
Subject: [PATCH] Oops, contig index is a zero not one based value

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@512 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 5f9ab1d92..42df2172c 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -292,7 +292,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
      *          at the end of the genome (no more contigs to jump to).
      */
     public boolean toNextContig() {
-        if (contigIndex < GenomeLoc.contigInfo.size()) {
+        if ((contigIndex + 1) < GenomeLoc.contigInfo.size()) {
             this.contigIndex++;
             this.start = 1;
             this.stop = 1;