INNER CODE UNIT · Python

get_args

nf-core/eager · bin/filter_bam_fragment_length.py:10

def get_args():
    """This function parses and return arguments passed in"""
    parser = argparse.ArgumentParser(
        prog="bam_filter", description="Filter bam on fragment length"
    )
    parser.add_argument("bam", help="Bam aligment file")
    parser.add_argument(
        "-l",
        dest="fraglen",
        default=35,
        type=int,
        help="Minimum fragment length. Default = 35",
    )
    parser.add_argument(
        "-a",
        dest="all",
        default=False,
        action="store_true",

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