Runs step8 (remove heterozygous haploid).

    :param in_prefix: the prefix of the input files.
    :param in_type: the type of the input files.
    :param out_prefix: the output prefix.
    :param base_dir: the output directory.
    :param options: the options needed.

    :type in_prefix: str
    :type in_type: str
    :type out_prefix: str
    :type base_dir: str
    :type options: list

    :returns: a tuple containing the prefix of the output files (the input
              prefix for the next script) and the type of the output files
              (``bfile``).

    This function calls the
    :py:mod:`pyGenClean.HeteroHap.remove_heterozygous_haploid` module. The
    required file type for this module is ``bfile``, hence the need to use the
    :py:func:`check_input_files` to check if the file input file type is the
    good one, or to create it if needed.

def run_remove_heterozygous_haploid(in_prefix, in_type, out_prefix, base_dir,
                                    options):
    """Runs step8 (remove heterozygous haploid).

    :param in_prefix: the prefix of the input files.
    :param in_type: the type of the input files.
    :param out_prefix: the output prefix.
    :param base_dir: the output directory.
    :param options: the options needed.

    :type in_prefix: str
    :type in_type: str
    :type out_prefix: str
    :type base_dir: str
    :type options: list

    :returns: a tuple containing the prefix of the output files (the input
              prefix for the next script) and the type of the output files
              (``bfile``).

    This function calls the
    :py:mod:`pyGenClean.HeteroHap.remove_heterozygous_haploid` module. The
    required file type for this module is ``bfile``, hence the need to use the
    :py:func:`check_input_files` to check if the file input file type is the
    good one, or to create it if needed.

    """
    # Creating the output directory
    os.mkdir(out_prefix)

    # We know we need bfile
    required_type = "bfile"
    check_input_files(in_prefix, in_type, required_type)

    # We need to inject the name of the input file and the name of the output
    # prefix
    script_prefix = os.path.join(out_prefix, "without_hh_genotypes")
    options += ["--{}".format(required_type), in_prefix,
                "--out", script_prefix]

    # We run the script
    try:
        remove_heterozygous_haploid.main(options)
    except remove_heterozygous_haploid.ProgramError as e:
        msg = "remove_heterozygous_haploid: {}".format(e)
        raise ProgramError(msg)

    # We get the number of genotypes that were set to missing
    nb_hh_missing = None
    with open(script_prefix + ".log", "r") as i_file:
        nb_hh_missing = re.search(
            r"(\d+) heterozygous haploid genotypes; set to missing",
            i_file.read(),
        )
    if nb_hh_missing:
        nb_hh_missing = int(nb_hh_missing.group(1))
    else:
        nb_hh_missing = 0

    # We write a LaTeX summary
    latex_file = os.path.join(script_prefix + ".summary.tex")
    try:
        with open(latex_file, "w") as o_file:
            print >>o_file, latex_template.subsection(
                remove_heterozygous_haploid.pretty_name
            )
            text = (
                "After Plink's heterozygous haploid analysis, a total of "
                "{:,d} genotype{} were set to missing.".format(
                    nb_hh_missing,
                    "s" if nb_hh_missing > 1 else "",
                )
            )
            print >>o_file, latex_template.wrap_lines(text)

    except IOError:
        msg = "{}: cannot write LaTeX summary".format(latex_file)
        raise ProgramError(msg)

    # Writing the summary results
    with open(os.path.join(base_dir, "results_summary.txt"), "a") as o_file:
        print >>o_file, "# {}".format(script_prefix)
        print >>o_file, ("Number of heterozygous haploid genotypes set to "
                         "missing\t{:,d}".format(nb_hh_missing))
        print >>o_file, "---"

    # We know this step produces an new data set (bfile), so we return it
    return _StepResult(
        next_file=os.path.join(out_prefix, "without_hh_genotypes"),
        next_file_type="bfile",
        latex_summary=latex_file,
        description=remove_heterozygous_haploid.desc,
        long_description=remove_heterozygous_haploid.long_desc,
        graph_path=None,
    )