def treds(args):
    """
    %prog treds hli.tred.tsv

    Compile allele_frequency for TREDs results. Write data.tsv, meta.tsv and
    mask.tsv in one go.
    """
    p = OptionParser(treds.__doc__)
    p.add_option("--csv", default=False, action="store_true",
                 help="Also write `meta.csv`")
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    tredresults, = args
    df = pd.read_csv(tredresults, sep="\t")

    tredsfile = datafile("TREDs.meta.csv")
    tf = pd.read_csv(tredsfile)

    tds = list(tf["abbreviation"])
    ids = list(tf["id"])
    tags = ["SampleKey"]
    final_columns = ["SampleKey"]
    afs = []
    for td, id in zip(tds, ids):
        tag1 = "{}.1".format(td)
        tag2 = "{}.2".format(td)
        if tag2 not in df:
            afs.append("{}")
            continue
        tags.append(tag2)
        final_columns.append(id)
        a = np.array(list(df[tag1]) + list(df[tag2]))
        counts = alleles_to_counts(a)
        af = counts_to_af(counts)
        afs.append(af)

    tf["allele_frequency"] = afs

    metafile = "TREDs_{}_SEARCH.meta.tsv".format(timestamp())
    tf.to_csv(metafile, sep="\t", index=False)
    logging.debug("File `{}` written.".format(metafile))
    if opts.csv:
        metacsvfile = metafile.rsplit(".", 1)[0] + ".csv"
        tf.to_csv(metacsvfile, index=False)
        logging.debug("File `{}` written.".format(metacsvfile))

    pp = df[tags]
    pp.columns = final_columns
    datafile = "TREDs_{}_SEARCH.data.tsv".format(timestamp())
    pp.to_csv(datafile, sep="\t", index=False)
    logging.debug("File `{}` written.".format(datafile))

    mask([datafile, metafile])
%prog treds hli.tred.tsv

    Compile allele_frequency for TREDs results. Write data.tsv, meta.tsv and
    mask.tsv in one go.