Prepare a delly-specific exclude file eliminating chromosomes.
    Delly wants excluded chromosomes listed as just the chromosome, with no coordinates.

def _delly_exclude_file(items, base_file, chrom):
    """Prepare a delly-specific exclude file eliminating chromosomes.
    Delly wants excluded chromosomes listed as just the chromosome, with no coordinates.
    """
    base_exclude = sshared.prepare_exclude_file(items, base_file, chrom)
    out_file = "%s-delly%s" % utils.splitext_plus(base_exclude)
    with file_transaction(items[0], out_file) as tx_out_file:
        with open(tx_out_file, "w") as out_handle:
            with open(base_exclude) as in_handle:
                for line in in_handle:
                    parts = line.split("\t")
                    if parts[0] == chrom:
                        out_handle.write(line)
                    else:
                        out_handle.write("%s\n" % parts[0])
    return out_file