Run CGI var to gVCF conversion from the command line.

def from_command_line():
    """
    Run CGI var to gVCF conversion from the 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)