From 2e89d5e46f6dd7f9cf61563cfa3fcc836307f6c4 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Apr 2009 20:05:24 +0000
Subject: [PATCH] That was an annoying bug to find.  Mark, I want a beer.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@293 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index ad1b2381b..21326424f 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -398,7 +398,8 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     }
 
     public final boolean isPast( GenomeLoc that ) {
-        return this.compareContigs(that) == 1 || this.getStart() > that.getStop();
+        int comparison = this.compareContigs(that);
+        return ( comparison == 1 || ( comparison == 0 && this.getStart() > that.getStop() ));
     }
 
     public final void incPos() {