From f32a32269c24caf46d90e65b3b238be48219f8d3 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 21 May 2010 20:13:36 +0000
Subject: [PATCH] minor change for eric

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/realignBamByChr.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/python/realignBamByChr.py b/python/realignBamByChr.py
index c1f9ec260..d26ce0e4a 100755
--- a/python/realignBamByChr.py
+++ b/python/realignBamByChr.py
@@ -34,7 +34,9 @@ def main():
     parser.add_option("-e", "--extraArgs", dest="extraArgs",
                         type="string", default=None,
                         help="")
-                        
+    parser.add_option("", "--dev", dest="dev",
+                        type='string', default="/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar",
+                        help="If provided, we'll use the GATK dev build")                        
     (OPTIONS, args) = parser.parse_args()
     if len(args) != 3:
         parser.error("incorrect number of arguments")
@@ -48,7 +50,7 @@ def main():
         if stage not in STAGES:
             sys.exit('unknown stage ' + stage)
 
-    myPipelineArgs = PipelineArgs(name = OPTIONS.name)
+    myPipelineArgs = PipelineArgs(name = OPTIONS.name, GATK_JAR = OPTIONS.dev)
     if ( OPTIONS.useB36 ):
         myPipelineArgs.ref = 'b36'