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]]
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]]