transform each read by identifying the barcode and UMI for each read
    and putting the information in the read name

def umi_transform(data):
    """
    transform each read by identifying the barcode and UMI for each read
    and putting the information in the read name
    """
    fqfiles = data["files"]
    fqfiles.extend(list(repeat("", 4-len(fqfiles))))
    fq1, fq2, fq3, fq4 = fqfiles
    umi_dir = os.path.join(dd.get_work_dir(data), "umis")
    safe_makedir(umi_dir)
    transform = dd.get_umi_type(data)
    if not transform:
        logger.info("No UMI transform specified, assuming pre-transformed data.")
        if is_transformed(fq1):
            logger.info("%s detected as pre-transformed, passing it on unchanged." % fq1)
            data["files"] = [fq1]
            return [[data]]
        else:
            logger.error("No UMI transform was specified, but %s does not look "
                         "pre-transformed." % fq1)
            sys.exit(1)

    if file_exists(transform):
        transform_file = transform
    else:
        transform_file = get_transform_file(transform)
        if not file_exists(transform_file):
            logger.error(
                "The UMI transform can be specified as either a file or a "
                "bcbio-supported transform. Either the file %s does not exist "
                "or the transform is not supported by bcbio. Supported "
                "transforms are %s."
                %(dd.get_umi_type(data), ", ".join(SUPPORTED_TRANSFORMS)))
            sys.exit(1)
    out_base = dd.get_sample_name(data) + ".umitransformed.fq.gz"
    out_file = os.path.join(umi_dir, out_base)
    if file_exists(out_file):
        data["files"] = [out_file]
        return [[data]]
    cellular_barcodes = get_cellular_barcodes(data)
    if len(cellular_barcodes) > 1:
        split_option = "--separate_cb"
    else:
        split_option = ""
    if dd.get_demultiplexed(data):
        demuxed_option = "--demuxed_cb %s" % dd.get_sample_name(data)
        split_option = ""
    else:
        demuxed_option = ""
    cores = dd.get_num_cores(data)
    # skip transformation if the file already looks transformed
    with open_fastq(fq1) as in_handle:
        read = next(in_handle)
        if "UMI_" in read:
            data["files"] = [out_file]
            return [[data]]
    locale_export = utils.locale_export()
    umis = _umis_cmd(data)
    cmd = ("{umis} fastqtransform {split_option} {transform_file} "
           "--cores {cores} {demuxed_option} "
           "{fq1} {fq2} {fq3} {fq4}"
           "| seqtk seq -L 20 - | gzip > {tx_out_file}")
    message = ("Inserting UMI and barcode information into the read name of %s"
               % fq1)
    with file_transaction(out_file) as tx_out_file:
        do.run(cmd.format(**locals()), message)
    data["files"] = [out_file]
    return [[data]]