Parses the command line options and arguments.

    :returns: A :py:class:`argparse.Namespace` object created by the
              :py:mod:`argparse` module. It contains the values of the
              different options.

    ===================== ====== =========================================
            Options        Type                Description
    ===================== ====== =========================================
    ``--file``            string The MBS file.
    ``--population-file`` string A file containing population information.
    ``--format``          string The output file format.
    ``--title``           string The title of the MDS plot.
    ``--xlabel``          string The label of the X axis.
    ``--ylabel``          string The label of the Y axis.
    ``--out``             string The prefix of the output files.
    ===================== ====== =========================================

    .. note::
        No option check is done here (except for the one automatically done by
        argparse). Those need to be done elsewhere (see :py:func:`checkArgs`).

def parseArgs():  # pragma: no cover
    """Parses the command line options and arguments.

    :returns: A :py:class:`argparse.Namespace` object created by the
              :py:mod:`argparse` module. It contains the values of the
              different options.

    ===================== ====== =========================================
            Options        Type                Description
    ===================== ====== =========================================
    ``--file``            string The MBS file.
    ``--population-file`` string A file containing population information.
    ``--format``          string The output file format.
    ``--title``           string The title of the MDS plot.
    ``--xlabel``          string The label of the X axis.
    ``--ylabel``          string The label of the Y axis.
    ``--out``             string The prefix of the output files.
    ===================== ====== =========================================

    .. note::
        No option check is done here (except for the one automatically done by
        argparse). Those need to be done elsewhere (see :py:func:`checkArgs`).

    """
    # The INPUT files
    group = parser.add_argument_group("Input File")
    group.add_argument("--file", type=str, metavar="FILE", required=True,
                       help="The MBS file.")
    parser.add_argument("--population-file", type=str, metavar="FORMAT",
                        required=True,
                        help="A file containing population information. "
                             "There must be three columns: famID, indID "
                             "and population information.")

    # The graphical options
    group = parser.add_argument_group("Graphical Options")
    addCustomOptions(group)

    # The OUTPUT files
    group = parser.add_argument_group("Output File")
    group.add_argument("--out", type=str, metavar="FILE",
                       default="mds",
                       help="The prefix of the output files. [default: "
                            "%(default)s]")

    args = parser.parse_args()

    return args