From c8d7207a8e90e4d9fddf4b77c7370d3779aa414f Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 22 Mar 2009 19:53:00 +0000
Subject: [PATCH] Fixed problem with GenomeLoc logic -- optimization was
 causing assertion failure.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@138 348d0f76-0448-11de-a6fe-93d51630548a
---
 core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 196162168..b570a08b3 100644
--- a/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -190,7 +190,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     {
         if ( thisContig == thatContig )
         {
-            assert(false);
+            // Optimization.  If the pointers are equal, then the contigs are equal.
             return 0;
         }