Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.

def _run_purecn(paired, work_dir):
    """Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
    """
    segfns = {"cnvkit": _segment_normalized_cnvkit, "gatk-cnv": _segment_normalized_gatk}
    out_base, out, all_files = _get_purecn_files(paired, work_dir)
    failed_file = out_base + "-failed.log"
    cnr_file = tz.get_in(["depth", "bins", "normalized"], paired.tumor_data)
    if not utils.file_uptodate(out["rds"], cnr_file) and not utils.file_exists(failed_file):
        cnr_file, seg_file = segfns[cnvkit.bin_approach(paired.tumor_data)](cnr_file, work_dir, paired)
        from bcbio import heterogeneity
        vcf_file = heterogeneity.get_variants(paired.tumor_data, include_germline=False)[0]["vrn_file"]
        vcf_file = germline.filter_to_pass_and_reject(vcf_file, paired, out_dir=work_dir)
        with file_transaction(paired.tumor_data, out_base) as tx_out_base:
            # Use UCSC style naming for human builds to support BSgenome
            genome = ("hg19" if dd.get_genome_build(paired.tumor_data) in ["GRCh37", "hg19"]
                      else dd.get_genome_build(paired.tumor_data))
            cmd = ["PureCN.R", "--seed", "42", "--out", tx_out_base, "--rds", "%s.rds" % tx_out_base,
                   "--sampleid", dd.get_sample_name(paired.tumor_data),
                   "--genome", genome,
                   "--vcf", vcf_file, "--tumor", cnr_file,
                   "--segfile", seg_file, "--funsegmentation", "Hclust", "--maxnonclonal", "0.3"]
            if dd.get_num_cores(paired.tumor_data) > 1:
                cmd += ["--cores", str(dd.get_num_cores(paired.tumor_data))]
            try:
                cmd = "export R_LIBS_USER=%s && %s && %s" % (utils.R_sitelib(), utils.get_R_exports(),
                                                             " ".join([str(x) for x in cmd]))
                do.run(cmd, "PureCN copy number calling")
            except subprocess.CalledProcessError as msg:
                if _allowed_errors(str(msg)):
                    logger.info("PureCN failed to find solution for %s: skipping" %
                                dd.get_sample_name(paired.tumor_data))
                    with open(failed_file, "w") as out_handle:
                        out_handle.write(str(msg))
                else:
                    logger.exception()
                    raise
            for f in all_files:
                if os.path.exists(os.path.join(os.path.dirname(tx_out_base), f)):
                    shutil.move(os.path.join(os.path.dirname(tx_out_base), f),
                                os.path.join(os.path.dirname(out_base), f))
    out = _get_purecn_files(paired, work_dir, require_exist=True)[1]
    return out if (out.get("rds") and os.path.exists(out["rds"])) else None