c264a73e401d5d030ee7ca510e2db7004418b469,scripts/cn_ztest.py,,,#,46

Before Change

    if args.target:
        antitarget_idx = cnarr["gene"].isin(cnvlib.params.ANTITARGET_ALIASES)
        if antitarget_idx.any():
            print("Ignoring", antitarget_idx.sum(), "off-target bins")
            cnarr = cnarr[~antitarget_idx]

    sig = ztest(cnarr, args.alpha)

After Change

    AP.add_argument("-t", "--target", action="store_true",
                    help="Test target bins only; ignore off-target bins.")

    AP.add_argument("-s", "--segment", metavar="FILENAME",
                    help=Segmentation calls (.cns), the output of the
                    "segment" command).)
    AP.add_argument("-y", "--male-reference", action="store_true",
                    help=Assume inputs were normalized to a male reference
                    (i.e. female samples will have +1 log-coverage of chrX;
                    otherwise male samples would have -1 chrX).)

Instances