def generate_macs_args(flags):
    """
    This is a helper function that takes the sim options and outputs the start the macs_args

    :param flags:
    :return macs_args:
    """
    macs_args = None
    if '-macs_file' in flags:
        macs_args = [flags['-macs_file'][0][0], flags['-length'][0][0], "-I", flags['-I'][0][0]]
    elif '-macsswig' in flags:
        macs_args = [flags['-macsswig'][0][0], flags['-length'][0][0], "-I", flags['-I'][0][0]]
    elif '-macs' in flags:
        macs_args = [flags['-macs'][0][0], flags['-length'][0][0], "-I", flags['-I'][0][0]]
    else:
        # This option should never be reached since it errors out in housekeeping
        print("There is no sim option given. Check your model file.")
        exit(1)
    return macs_args