From b8a6f6e83046bf990d69bfbe2ca401b3f685cda9 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 22 Apr 2009 19:39:07 +0000 Subject: [PATCH] Support for indexBAM command git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@496 348d0f76-0448-11de-a6fe-93d51630548a --- python/MergeBAMBatch.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/MergeBAMBatch.py b/python/MergeBAMBatch.py index e39bceee0..b8535f3d7 100755 --- a/python/MergeBAMBatch.py +++ b/python/MergeBAMBatch.py @@ -5,6 +5,7 @@ from optparse import OptionParser from datetime import date import glob import operator +import ValidateGATK MERGE_BIN = '/seq/software/picard/current/bin/MergeSamFiles.jar' bam_ext = '.bam' @@ -40,7 +41,7 @@ if __name__ == "__main__": sources = reduce( operator.__add__, map( glob.glob, s[1:] ), [] ) if OPTIONS.ignoreExistingFiles or not os.path.exists(stamped_filename): - cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' O=' + stamped_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources)) + cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' AS=true O=' + stamped_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources)) print cmd farm_commands.cmd(cmd, OPTIONS.farm_sub, output) @@ -48,4 +49,5 @@ if __name__ == "__main__": print 'os.path.exists(current_link)', os.path.exists(current_link) cmd = 'ln -s ' + stamped_filename + " " + current_link farm_commands.cmd(cmd, False, '') + ValidateGATK.indexBAM(current_link)