Filter and annotate somatic VCFs with damage/bias artifacts on low frequency variants.

    Moves damage estimation to INFO field, instead of leaving in FILTER.

def run_filter(vrn_file, align_bam, ref_file, data, items):
    """Filter and annotate somatic VCFs with damage/bias artifacts on low frequency variants.

    Moves damage estimation to INFO field, instead of leaving in FILTER.
    """
    if not should_filter(items) or not vcfutils.vcf_has_variants(vrn_file):
        return data
    else:
        raw_file = "%s-damage.vcf" % utils.splitext_plus(vrn_file)[0]
        out_plot_files = ["%s%s" % (utils.splitext_plus(raw_file)[0], ext)
                          for ext in ["_seq_bias_simplified.pdf", "_pcr_bias_simplified.pdf"]]
        if not utils.file_uptodate(raw_file, vrn_file) and not utils.file_uptodate(raw_file + ".gz", vrn_file):
            with file_transaction(items[0], raw_file) as tx_out_file:
                # Does not apply --qcSummary plotting due to slow runtimes
                cmd = ["dkfzbiasfilter.py", "--filterCycles", "1", "--passOnly",
                       "--tempFolder", os.path.dirname(tx_out_file),
                       vrn_file, align_bam, ref_file, tx_out_file]
                do.run(cmd, "Filter low frequency variants for DNA damage and strand bias")
                for out_plot in out_plot_files:
                    tx_plot_file = os.path.join("%s_qcSummary" % utils.splitext_plus(tx_out_file)[0], "plots",
                                                os.path.basename(out_plot))
                    if utils.file_exists(tx_plot_file):
                        shutil.move(tx_plot_file, out_plot)
        raw_file = vcfutils.bgzip_and_index(raw_file, items[0]["config"])
        data["vrn_file"] = _filter_to_info(raw_file, items[0])
        out_plot_files = [x for x in out_plot_files if utils.file_exists(x)]
        data["damage_plots"] = out_plot_files
        return data