docs: 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