sam-discard-dups.py 文件源码

def parse_command_line():
    # Define parameters
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="SAM - Discard duplicates/multiple-mappers",
        version=version_info,
        epilog="""
This script reads a SAM file, and discards ALL reads which map
multiple times (does not keep even one of the mapping locations).

TODO: Explain hard-clipped reads in minION runs

Example:
    # Remove all duplicated reads dirnames:

    $ %(prog)s input.sam > output.no-dups.sam

        """)


    # Positional parameter
    parser.add_argument('filename', metavar='FILE', help='file to process');
    args = parser.parse_args()

    return args