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Support for indexBAM command 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@496 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-22 19:39:07 +00:00
parent d99d67d51c
commit b8a6f6e830
1 changed files with 3 additions and 1 deletions
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4
python/MergeBAMBatch.py
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@ -5,6 +5,7 @@ from optparse import OptionParser
from datetime import date from datetime import date
import glob import glob
import operator import operator
import ValidateGATK
MERGE_BIN = '/seq/software/picard/current/bin/MergeSamFiles.jar' MERGE_BIN = '/seq/software/picard/current/bin/MergeSamFiles.jar'
bam_ext = '.bam' bam_ext = '.bam'
@ -40,7 +41,7 @@ if __name__ == "__main__":
sources = reduce( operator.__add__, map( glob.glob, s[1:] ), [] ) sources = reduce( operator.__add__, map( glob.glob, s[1:] ), [] )
if OPTIONS.ignoreExistingFiles or not os.path.exists(stamped_filename): 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 print cmd
farm_commands.cmd(cmd, OPTIONS.farm_sub, output) 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) print 'os.path.exists(current_link)', os.path.exists(current_link)
cmd = 'ln -s ' + stamped_filename + " " + current_link cmd = 'ln -s ' + stamped_filename + " " + current_link
farm_commands.cmd(cmd, False, '') farm_commands.cmd(cmd, False, '')
ValidateGATK.indexBAM(current_link)