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

Before Change

    target_chroms = dict(tabio.read_auto(target_bed).by_chromosome())
    if access_bed:
        // Chromosomes" accessible sequence regions are given -- use them
        access_chroms = dict(tabio.read_auto(access_bed).by_chromosome())
        if access_chroms and set(access_chroms).isdisjoint(target_chroms):
            raise ValueError("Chromosome names in the accessible regions file "
                             "%s %r do not match those in targets %s %r"
                             % (access_bed,

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