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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def _run_qc_tools(bam_file, data):
 """Run a set of third party quality control tools, returning QC directory and metrics. :param bam_file: alignments in bam format :param data: dict with all configuration information :returns: dict with output of different tools """

    from bcbio.qc import (atropos, contamination, coverage, damage, fastqc, kraken,
                          qsignature, qualimap, samtools, picard, srna, umi, variant,
                          viral, preseq, chipseq)
    tools = {"fastqc": fastqc.run,
             "atropos": atropos.run,
             "small-rna": srna.run,
             "samtools": samtools.run,
             "qualimap": qualimap.run,
             "qualimap_rnaseq": qualimap.run_rnaseq,
             "qsignature": qsignature.run,
             "contamination": contamination.run,
             "coverage": coverage.run,
             "damage": damage.run,
             "variants": variant.run,
             "peddy": peddy.run_qc,
             "kraken": kraken.run,
             "picard": picard.run,
             "umi": umi.run,
             "viral": viral.run,
             "preseq": preseq.run,
             "chipqc": chipseq.run
             }
    qc_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "qc", data["description"]))
    metrics = {}
    qc_out = utils.deepish_copy(dd.get_summary_qc(data))
    for program_name in dd.get_algorithm_qc(data):
        if not bam_file and program_name != "kraken":  # kraken doesn't need bam
            continue
        if dd.get_phenotype(data) == "germline" and program_name != "variants":
            continue
        qc_fn = tools[program_name]
        cur_qc_dir = os.path.join(qc_dir, program_name)
        out = qc_fn(bam_file, data, cur_qc_dir)
        qc_files = None
        if out and isinstance(out, dict):
            # Check for metrics output, two cases:
            # 1. output with {"metrics"} and files ("base")
            if "metrics" in out:
                metrics.update(out.pop("metrics"))
            # 2. a dictionary of metrics
            elif "base" not in out:
                metrics.update(out)
            # Check for files only output
            if "base" in out:
                qc_files = out
        elif out and isinstance(out, six.string_types) and os.path.exists(out):
            qc_files = {"base": out, "secondary": []}
        if not qc_files:
            qc_files = _organize_qc_files(program_name, cur_qc_dir)
        if qc_files:
            qc_out[program_name] = qc_files

    metrics["Name"] = dd.get_sample_name(data)
    metrics["Quality format"] = dd.get_quality_format(data).lower()
    return {"qc": qc_out, "metrics": metrics}