From 022832bd74f32b8edb0663fc64034fa45265f0f1 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 21 Nov 2011 14:49:47 -0500
Subject: [PATCH] Very bad use of the == operator with Strings was ensuring
 that validating GenomeLocs was very inefficient.  This fix resulted in a
 significant speedup for a simple RodWalker.

---
 .../src/org/broadinstitute/sting/utils/GenomeLocParser.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 8cba183da..4f1df9e7b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -87,12 +87,12 @@ public class GenomeLocParser {
 
         @Requires("contig != null")
         public synchronized boolean hasContig(final String contig) {
-            return lastContig == contig || dict.getSequence(contig) != null;
+            return contig.equals(lastContig) || dict.getSequence(contig) != null;
         }
 
         @Requires("index >= 0")
         public synchronized boolean hasContig(final int index) {
-            return lastIndex == index|| dict.getSequence(index) != null;
+            return lastIndex == index || dict.getSequence(index) != null;
         }
 
         @Requires("contig != null")