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Configurable execution path at same location as BAM input. #71

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Configurable execution path at same location as BAM input. #71

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7 changes: 1 addition & 6 deletions parliament2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,18 +58,13 @@ def run_parliament(bam, bai, ref_genome, fai, prefix, filter_short_contigs, brea

def main():
args = parse_arguments()

prefix = args.prefix
if prefix is None:
if args.bam.endswith(".bam"):
prefix = args.bam[:-4]
else:
prefix = args.bam[:-5]
if not args.bam.startswith("/home/dnanexus/in/"):
args.bam = "/home/dnanexus/in/{0}".format(args.bam)
args.bai = "/home/dnanexus/in/{0}".format(args.bai)
args.ref_genome = "/home/dnanexus/in/{0}".format(args.ref_genome)
args.fai = "/home/dnanexus/in/{0}".format(args.fai)

ref_genome_name = gunzip_input(args.ref_genome)

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