AMBER: calculate allele frequencies at likely heterozygous sites.

    lenient flag allows amber runs on small test sets.

def _run_amber(paired, work_dir, lenient=False):
    """AMBER: calculate allele frequencies at likely heterozygous sites.

    lenient flag allows amber runs on small test sets.
    """
    amber_dir = utils.safe_makedir(os.path.join(work_dir, "amber"))
    out_file = os.path.join(amber_dir, "%s.amber.baf" % dd.get_sample_name(paired.tumor_data))
    if not utils.file_exists(out_file) or not utils.file_exists(out_file + ".pcf"):
        with file_transaction(paired.tumor_data, out_file) as tx_out_file:
            key = "germline_het_pon"
            het_bed = tz.get_in(["genome_resources", "variation", key], paired.tumor_data)
            cmd = ["AMBER"] + _get_jvm_opts(tx_out_file, paired.tumor_data) + \
                  ["-threads", dd.get_num_cores(paired.tumor_data),
                   "-tumor", dd.get_sample_name(paired.tumor_data),
                   "-tumor_bam", dd.get_align_bam(paired.tumor_data),
                   "-reference", dd.get_sample_name(paired.normal_data),
                   "-reference_bam", dd.get_align_bam(paired.normal_data),
                   "-ref_genome", dd.get_ref_file(paired.tumor_data),
                   "-bed", het_bed,
                   "-output_dir", os.path.dirname(tx_out_file)]
            if lenient:
                cmd += ["-max_het_af_percent", "1.0"]
            try:
                do.run(cmd, "PURPLE: AMBER baf generation")
            except subprocess.CalledProcessError as msg:
                if not lenient and _amber_allowed_errors(str(msg)):
                    return _run_amber(paired, work_dir, True)
            for f in os.listdir(os.path.dirname(tx_out_file)):
                if f != os.path.basename(tx_out_file):
                    shutil.move(os.path.join(os.path.dirname(tx_out_file), f),
                                os.path.join(amber_dir, f))
    return out_file