Run theta, calculating subpopulations and normal contamination.

def _run_theta(cnv_info, data, work_dir, run_n3=True):
    """Run theta, calculating subpopulations and normal contamination.
    """
    out = {"caller": "theta"}
    max_normal = "0.9"
    opts = ["-m", max_normal]
    n2_result = _safe_run_theta(cnv_info["theta_input"], os.path.join(work_dir, "n2"), ".n2.results",
                                ["-n", "2"] + opts, data)
    if n2_result:
        out["estimate"] = n2_result
        if run_n3:
            n2_bounds = "%s.withBounds" % os.path.splitext(n2_result)[0]
            n3_result = _safe_run_theta(n2_bounds, os.path.join(work_dir, "n3"), ".n3.results",
                                        ["-n", "3", "--RESULTS", n2_result] + opts,
                                        data)
            if n3_result:
                best_result = _select_model(n2_bounds, n2_result, n3_result,
                                            os.path.join(work_dir, "n3"), data)
                out["estimate"] = best_result
                out["cnvs"] = _merge_theta_calls(n2_bounds, best_result, cnv_info["vrn_file"], data)
    return out