Validation with hap.py: https://github.com/Illumina/hap.py

    XXX Does not yet parse out metrics for plotting.

def _run_happy_eval(vrn_file, rm_file, rm_interval_file, base_dir, data):
    """Validation with hap.py: https://github.com/Illumina/hap.py

    XXX Does not yet parse out metrics for plotting.
    """
    out_dir = utils.safe_makedir(os.path.join(base_dir, "happy"))
    out_prefix = os.path.join(out_dir, "val")
    if not utils.file_exists(out_prefix + ".summary.csv"):
        vrn_file, rm_file, interval_bed = _prepare_inputs(vrn_file, rm_file, rm_interval_file, base_dir, data)
        cmd = ["hap.py", "-V", "-f", interval_bed, "-r", dd.get_ref_file(data),
               "-l", ",".join(_get_location_list(interval_bed)),
               "-o", out_prefix, rm_file, vrn_file]
        do.run(cmd, "Validate calls using hap.py", data)
    return {"vcf": out_prefix + ".vcf.gz"}