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Actually has working version of the python script to merge multiple bam files 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@530 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-24 19:15:55 +00:00
parent 40a2b3eeb3
commit 3739682bef
1 changed files with 7 additions and 10 deletions
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17
python/MergeBAMBatch.py
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@ -36,18 +36,15 @@ if __name__ == "__main__":
if ( s <> [] and s[0] <> '#' ):
merged_filename = s[0]
output = os.path.join(directory, merged_filename + '.stdout')
current_link = os.path.join(directory, merged_filename + bam_ext)
stamped_filename = os.path.join(directory, merged_filename + '_' + time_stamp + bam_ext)
output_filename = os.path.join(directory, merged_filename + bam_ext)
output_index = output_filename + ".bai"
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 + ' AS=true O=' + stamped_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
if OPTIONS.ignoreExistingFiles or not os.path.exists(output_filename):
cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' AS=true O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
print cmd
farm_commands.cmd(cmd, OPTIONS.farm_sub, output)
if OPTIONS.ignoreExistingFiles or not os.path.lexists(current_link):
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)
if OPTIONS.ignoreExistingFiles or not os.path.exists(output_index):
ValidateGATK.indexBAM(output_filename)