031c390686da59ea8144c69380bf9d5a1e8d1743,cnvlib/reference.py,,do_reference,#Any#Any#Any#Any#Any#Any#Any#Any#,17

Before Change

        // guaranteed to exist, infer from those first, then replace those
        // values where antitargets are suitable.
        sexes = infer_sexes(target_fnames, male_reference)
        if antitarget_fnames:
            sexes.update(infer_sexes(antitarget_fnames, male_reference))
    else:
        sexes = collections.defaultdict(lambda: female_samples)

    // Calculate & save probe centers

After Change

            a_sexes = infer_sexes(antitarget_fnames, male_reference)
            for sid, a_is_xx in a_sexes.items():
                t_is_xx = sexes.get(sid)
                if t_is_xx is None:
                    sexes[sid] = a_is_xx
                elif t_is_xx != a_is_xx and a_is_xx is not None:
                    logging.warning("Sample %s chromosomal X/Y ploidy looks "
                                    "like %s in targets but %s in antitargets; "
                                    "preferring antitargets",
                                    sid,
                                    "female" if t_is_xx else "male",
                                    "female" if a_is_xx else "male")
                    sexes[sid] = a_is_xx
    else:
        sexes = collections.defaultdict(lambda: female_samples)

    // Calculate & save probe centers

Instances