From 165e504d1c8ba5d7d5717996631e93d41e2af92e Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Apr 2009 19:45:47 +0000
Subject: [PATCH] Turn on new TraverseLociByReference is now only dependent on
 the -et flag.  REGION_STR does not matter.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 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 a7378b076..0512d487a 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -262,7 +262,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
                 if ( WALK_ALL_LOCI ) {
                     // TODO: Temporary debugging code.  Activate the new debugging code only when the MicroManager
                     //                                  is not filtered.
-                    if( ENABLE_THREADING && REGION_STR == null ) {
+                    if( ENABLE_THREADING ) {
                         logger.warn("Preliminary threading support enabled");
                         microManager = new MicroManager( INPUT_FILE, REF_FILE_ARG, numThreads );
                         this.engine = microManager.getTraversalEngine();