code: def from_command_line():
      
      # Parse options
      parser = argparse.ArgumentParser(
          description='Convert Complete Genomics var files to gVCF format.')
      parser.add_argument(
          '-d', '--refseqdir', metavar='REFSEQDIR', required=True,
          dest='refseqdir',
          help='Directory twobit reference genomes files are stored.')
      parser.add_argument(
          '-i', '--input', metavar='INPUTVARFILE',
          dest='cgivarfile',
          help='Path to Complete Genomics var file to convert. If omitted, data '
          ' also be piped in as standard input.')
      parser.add_argument(
          '-o', '--output', metavar='OUTPUTVCFFILE',
          dest='vcfoutfile',
          help='Path to where to save output VCF file.')
      parser.add_argument(
          '-D', '--download', action='store_true', dest='downloadrefseq',
          help='Download the 2bit file from UCSC to REFSEQDIR, if needed.')
      parser.add_argument(
          '-v', '--var-only', action='store_true', dest='varonly',
          help='Only report variant lines (i.e. VCF, but not gVCF)')
      args = parser.parse_args()
  
      # Get local twobit file from its directory. Download and store if needed.
      twobit_path, twobit_name = get_reference_genome_file(
          args.refseqdir, build='b37')
      # Handle input
      if sys.stdin.isatty():  # false if data is piped in
          var_input = args.cgivarfile
      else:
          var_input = sys.stdin
      # Handle output
      if args.vcfoutfile:
          convert_to_file(var_input,
                          args.vcfoutfile,
                          twobit_path,
                          twobit_name,
                          args.varonly)
      else:
          for line in convert(
                  cgi_input=var_input,
                  twobit_ref=twobit_path,
                  twobit_name=twobit_name,
                  var_only=args.varonly):
              print(line)
docs: Run CGI var to gVCF conversion from the command line.