Calculate coverage in an CNVkit ready format using mosdepth.

def _calculate_sv_coverage_cnvkit(data, work_dir):
    """Calculate coverage in an CNVkit ready format using mosdepth.
    """
    from bcbio.variation import coverage
    from bcbio.structural import annotate
    out_target_file = os.path.join(work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
    out_anti_file = os.path.join(work_dir, "%s-antitarget-coverage.cnn" % dd.get_sample_name(data))
    if ((not utils.file_exists(out_target_file) or not utils.file_exists(out_anti_file)) and
          (dd.get_align_bam(data) or dd.get_work_bam(data))):
        target_cov = coverage.run_mosdepth(data, "target", tz.get_in(["regions", "bins", "target"], data))
        anti_cov = coverage.run_mosdepth(data, "antitarget", tz.get_in(["regions", "bins", "antitarget"], data))
        target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
        out_target_file = _add_log2_depth(target_cov_genes, out_target_file, data)
        out_anti_file = _add_log2_depth(anti_cov.regions, out_anti_file, data)
    return out_target_file, out_anti_file