Prepare a sample to be run, potentially converting from BAM to
    FASTQ and/or downsampling the number of reads for a test run

def prepare_sample(data):
    """Prepare a sample to be run, potentially converting from BAM to
    FASTQ and/or downsampling the number of reads for a test run
    """
    data = utils.to_single_data(data)
    logger.debug("Preparing %s" % data["rgnames"]["sample"])
    data["files"] = get_fastq_files(data)
    # get_fastq_files swaps over quality scores to standard, unless trimming
    if not(dd.get_trim_reads(data)):
        data = dd.set_quality_format(data, "standard")
    return [[data]]