Provide GC annotated intervals for error correction during panels and denoising.

    TODO: include mappability and segmentation duplication inputs

def annotate_intervals(target_file, data):
    """Provide GC annotated intervals for error correction during panels and denoising.

    TODO: include mappability and segmentation duplication inputs
    """
    out_file = "%s-gcannotated.tsv" % utils.splitext_plus(target_file)[0]
    if not utils.file_uptodate(out_file, target_file):
        with file_transaction(data, out_file) as tx_out_file:
            params = ["-T", "AnnotateIntervals", "-R", dd.get_ref_file(data),
                      "-L", target_file,
                      "--interval-merging-rule", "OVERLAPPING_ONLY",
                      "-O", tx_out_file]
            _run_with_memory_scaling(params, tx_out_file, data)
    return out_file