Run qualimap for a rnaseq bam file and parse results

def run_rnaseq(bam_file, data, out_dir):
    """
    Run qualimap for a rnaseq bam file and parse results
    """
    strandedness = {"firststrand": "strand-specific-reverse",
                    "secondstrand": "strand-specific-forward",
                    "unstranded": "non-strand-specific"}

    # Qualimap results should be saved to a directory named after sample.
    # MultiQC (for parsing additional data) picks the sample name after the dir as follows:
    #   <sample name>/raw_data_qualimapReport/insert_size_histogram.txt
    results_dir = os.path.join(out_dir, dd.get_sample_name(data))
    results_file = os.path.join(results_dir, "rnaseq_qc_results.txt")
    report_file = os.path.join(results_dir, "qualimapReport.html")
    config = data["config"]
    gtf_file = dd.get_gtf_file(data)
    library = strandedness[dd.get_strandedness(data)]
    if not utils.file_exists(results_file):
        with file_transaction(data, results_dir) as tx_results_dir:
            utils.safe_makedir(tx_results_dir)
            bam.index(bam_file, config)
            cmd = _rnaseq_qualimap_cmd(data, bam_file, tx_results_dir, gtf_file, library)
            do.run(cmd, "Qualimap for {}".format(dd.get_sample_name(data)))
            tx_results_file = os.path.join(tx_results_dir, "rnaseq_qc_results.txt")
            cmd = "sed -i 's/bam file = .*/bam file = %s.bam/' %s" % (dd.get_sample_name(data), tx_results_file)
            do.run(cmd, "Fix Name Qualimap for {}".format(dd.get_sample_name(data)))
    metrics = _parse_rnaseq_qualimap_metrics(report_file)
    metrics.update(_detect_duplicates(bam_file, results_dir, data))
    metrics.update(_detect_rRNA(data, results_dir))
    metrics.update({"Average_insert_size": salmon.estimate_fragment_size(data)})
    metrics = _parse_metrics(metrics)
    # Qualimap output folder (results_dir) needs to be named after the sample (see comments above). However, in order
    # to keep its name after upload, we need to put  the base QC file (results_file) into the root directory (out_dir):
    base_results_file = os.path.join(out_dir, os.path.basename(results_file))
    shutil.copyfile(results_file, base_results_file)
    return {"base": base_results_file,
            "secondary": _find_qualimap_secondary_files(results_dir, base_results_file),
            "metrics": metrics}