From 1e2e78265df86cbe47019b1569aa44b32f4df9c5 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 26 Apr 2009 18:15:42 +0000
Subject: [PATCH] Inadvertently removed interval file support in new TbLbR. 
 Fixed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@540 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index d8f66489a..2b77f44b1 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -333,7 +333,11 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         engine.initialize();
 
         if( microScheduler != null ) {
-            List<GenomeLoc> locs = GenomeLoc.parseGenomeLocs( REGION_STR );
+            List<GenomeLoc> locs = null;
+            if (INTERVALS_FILE != null)
+                locs = GenomeLoc.IntervalFileToList(INTERVALS_FILE);
+            else
+                locs = GenomeLoc.parseGenomeLocs( REGION_STR );
             microScheduler.execute( my_walker, locs );
         }
         else