Create a final output file with merged CNVkit and THetA copy and population estimates.

def _merge_theta_calls(bounds_file, result_file, cnv_file, data):
    """Create a final output file with merged CNVkit and THetA copy and population estimates.
    """
    out_file = "%s-merged.txt" % (result_file.replace(".BEST.results", ""))
    if not utils.file_uptodate(out_file, result_file):
        with file_transaction(data, out_file) as tx_out_file:
            updater = _update_with_calls(result_file, cnv_file)
            with open(bounds_file) as in_handle:
                with open(tx_out_file, "w") as out_handle:
                    i = 0
                    for line in in_handle:
                        if line.startswith("#"):
                            parts = line.rstrip().split("\t")
                            parts += ["cnv", "pop_cnvs", "pop_pvals"]
                            out_handle.write("\t".join(parts) + "\n")
                        else:
                            out_handle.write(updater(i, line))
                            i += 1
    return out_file