From c7777d46d654884ca107c1426bd6ae3e4221310d Mon Sep 17 00:00:00 2001
From: kcibul <kcibul@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 12 Apr 2009 02:44:14 +0000
Subject: [PATCH] * re-enabled setting of sequence dictionary information on
 GenomeLoc

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index 27cc67aa4..9419c0241 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -273,7 +273,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         // Prepare the sort ordering w.r.t. the sequence dictionary
         if (REF_FILE_ARG != null) {
             final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
-            //GenomeLoc.setupRefContigOrdering(refFile);
+            GenomeLoc.setupRefContigOrdering(refFile);
         }
 
         // Determine the validation stringency.  Default to ValidationStringency.STRICT.