6372bff538de67595fda0183964a8df4b9b105fb,cnvlib/antitarget.py,,get_background,#Any#Any#Any#Any#,13

Before Change

                                target_bed,
                                tuple(sorted(target_chroms.keys())[:3])))
        // But filter out untargeted alternative contigs and mitochondria
        untgt_chroms = set(access_chroms) - set(target_chroms)
        // Autosomes typically have numeric names, allosomes are X and Y
        is_canonical = re.compile(r"(chr)?(\d+|[XYxy])$")
        if any(is_canonical.match(c) for c in target_chroms):
            chroms_to_skip = [c for c in untgt_chroms

After Change

            max_tgt_chr_name_len = max(map(len, target_chroms))
            chroms_to_skip = [c for c in untgt_chroms
                              if len(c) > max_tgt_chr_name_len]
        if chroms_to_skip:
            logging.info("Skipping untargeted chromosomes %s",
                         " ".join(sorted(chroms_to_skip)))
            skip_idx = accessible.chromosome.isin(chroms_to_skip)
            accessible = accessible[~skip_idx]
    else:
        // Chromosome accessible sequence regions not known -- use heuristics
        // (chromosome length is endpoint of last probe; skip initial
        // <magic number> of bases that are probably telomeric)

Instances