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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 _freebayes_cutoff(in_file, data):
 """Perform filtering of FreeBayes results, flagging low confidence calls. Filters using cutoffs on low depth based on Meynert et al's work modeling sensitivity of homozygote and heterozygote calling on depth: http://www.ncbi.nlm.nih.gov/pubmed/23773188 and high depth heterozygote SNP filtering based on Heng Li's work evaluating variant calling artifacts: http://arxiv.org/abs/1404.0929 Tuned based on NA12878 call comparisons to Genome in a Bottle reference genome. """

    if not vcfutils.vcf_has_variants(in_file):
        base, ext = utils.splitext_plus(in_file)
        out_file = "{base}-filter{ext}".format(**locals())
        if not utils.file_exists(out_file):
            shutil.copy(in_file, out_file)
        if out_file.endswith(".vcf.gz"):
            out_file = vcfutils.bgzip_and_index(out_file, data["config"])
        return out_file

    depth_thresh, qual_thresh = None, None
    if _do_high_depth_filter(data):
        stats = _calc_vcf_stats(in_file)
        if stats["avg_depth"] > 0:
            depth_thresh = int(math.ceil(stats["avg_depth"] + 3 * math.pow(stats["avg_depth"], 0.5)))
            qual_thresh = depth_thresh * 2.0  # Multiplier from default GATK QD cutoff filter
    filters = ('(AF[0] <= 0.5 && (max(FORMAT/DP) < 4 || (max(FORMAT/DP) < 13 && %QUAL < 10))) || '
               '(AF[0] > 0.5 && (max(FORMAT/DP) < 4 && %QUAL < 50))')
    if depth_thresh:
        filters += ' || (%QUAL < {qual_thresh} && max(FORMAT/DP) > {depth_thresh} && AF[0] <= 0.5)'.format(**locals())
    return cutoff_w_expression(in_file, filters, data, name="FBQualDepth")