Call copy numbers from a normalized and segmented input file.

def call_copy_numbers(seg_file, work_dir, data):
    """Call copy numbers from a normalized and segmented input file.
    """
    out_file = os.path.join(work_dir, "%s-call.seg" % dd.get_sample_name(data))
    if not utils.file_exists(out_file):
        with file_transaction(data, out_file) as tx_out_file:
            params = ["-T", "CallCopyRatioSegments",
                      "-I", seg_file, "-O", tx_out_file]
            _run_with_memory_scaling(params, tx_out_file, data)
    return out_file