def get_options():
    """ get the command line options
    """
    
    parser = argparse.ArgumentParser(description="Script to batch process de"
        "novo clustering.")
    parser.add_argument("--in", dest="input", required=True, help="Path to"
        "file listing known mutations in genes. See example file in data folder"
        "for format.")
    parser.add_argument("--temp-dir", required=True, help="path to hold intermediate files")
    parser.add_argument("--out", required=True, help="Path to output file.")
    
    args = parser.parse_args()
    
    return args
get the command line options