1281963269c819f22fed98583526df8946d18b4a,cnvlib/commands.py,,do_import_theta,#Any#Any#Any#,1660

Before Change

    for copies in theta["C"]:
        // Replace segment values with these integers
        // Drop any segments where the C value is None
        new_segs = []
        for seg, ncop in zip(segarr.copy(), copies):
            if ncop is None:
                continue
            new_segs.append(seg._replace(

After Change

    theta = importers.parse_theta_results(theta_results_fname)
    for copies in theta["C"]:
        // Drop any segments where the C value is None
        mask_drop = np.array([c is None for c in copies], dtype="bool")
        segarr = segarr[~mask_drop].copy()
        ok_copies = np.array([c for c in copies if c is not None], dtype="int")
        // Replace remaining segment values with these integers
        segarr["cn"] = ok_copies.copy()
        ok_copies[ok_copies == 0] = 0.5
        segarr["log2"] = np.log2(ok_copies / ploidy)
        segarr.sort_columns()
        yield segarr

Instances