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minor change for eric 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-05-21 20:13:36 +00:00
parent b10950c691
commit f32a32269c
1 changed files with 4 additions and 2 deletions
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6
python/realignBamByChr.py
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@ -34,7 +34,9 @@ def main():
parser.add_option("-e", "--extraArgs", dest="extraArgs", parser.add_option("-e", "--extraArgs", dest="extraArgs",
type="string", default=None, type="string", default=None,
help="") 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() (OPTIONS, args) = parser.parse_args()
if len(args) != 3: if len(args) != 3:
parser.error("incorrect number of arguments") parser.error("incorrect number of arguments")
@ -48,7 +50,7 @@ def main():
if stage not in STAGES: if stage not in STAGES:
sys.exit('unknown stage ' + stage) sys.exit('unknown stage ' + stage)
myPipelineArgs = PipelineArgs(name = OPTIONS.name) myPipelineArgs = PipelineArgs(name = OPTIONS.name, GATK_JAR = OPTIONS.dev)
if ( OPTIONS.useB36 ): if ( OPTIONS.useB36 ):
myPipelineArgs.ref = 'b36' myPipelineArgs.ref = 'b36'