Runs Plink with the geno option.

    :param options: the options.

    :type options: argparse.Namespace

def runPlink(options):
    """Runs Plink with the geno option.

    :param options: the options.

    :type options: argparse.Namespace

    """
    # The plink command
    plinkCommand = ["plink", "--noweb", "--bfile", options.bfile, "--geno",
                    str(options.geno), "--make-bed", "--out", options.out]

    output = None
    try:
        output = subprocess.check_output(plinkCommand,
                                         stderr=subprocess.STDOUT, shell=False)
    except subprocess.CalledProcessError:
        msg = "plink: couldn't run plink"
        raise ProgramError(msg)