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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 _square_batch_bcbio_variation(data, region, bam_files, vrn_files, out_file, todo="square"):
 """Run squaring or merging analysis using bcbio.variation.recall. """

    ref_file = tz.get_in(("reference", "fasta", "base"), data)
    cores = tz.get_in(("config", "algorithm", "num_cores"), data, 1)
    resources = config_utils.get_resources("bcbio-variation-recall", data["config"])
    # adjust memory by cores but leave room for run program memory
    memcores = int(math.ceil(float(cores) / 5.0))
    jvm_opts = config_utils.adjust_opts(resources.get("jvm_opts", ["-Xms250m", "-Xmx2g"]),
                                        {"algorithm": {"memory_adjust": {"direction": "increase",
                                                                         "magnitude": memcores}}})
    # Write unique VCFs and BAMs to input file
    input_file = "%s-inputs.txt" % os.path.splitext(out_file)[0]
    with open(input_file, "w") as out_handle:
        out_handle.write("\n".join(sorted(list(set(vrn_files)))) + "\n")
        if todo == "square":
            out_handle.write("\n".join(sorted(list(set(bam_files)))) + "\n")
    variantcaller = tz.get_in(("config", "algorithm", "jointcaller"), data).replace("-joint", "")
    cmd = ["bcbio-variation-recall", todo] + jvm_opts + broad.get_default_jvm_opts() + \
          ["-c", cores, "-r", bamprep.region_to_gatk(region)]
    if todo == "square":
        cmd += ["--caller", variantcaller]
    cmd += [out_file, ref_file, input_file]
    bcbio_env = utils.get_bcbio_env()
    cmd = " ".join(str(x) for x in cmd)
    do.run(cmd, "%s in region: %s" % (cmd, bamprep.region_to_gatk(region)), env=bcbio_env)
    return out_file