code: def get_sv_chroms(items, exclude_file):
      
      exclude_regions = {}
      for region in pybedtools.BedTool(exclude_file):
          if int(region.start) == 0:
              exclude_regions[region.chrom] = int(region.end)
      out = []
      with pysam.Samfile(dd.get_align_bam(items[0]) or dd.get_work_bam(items[0]))as pysam_work_bam:
          for chrom, length in zip(pysam_work_bam.references, pysam_work_bam.lengths):
              exclude_length = exclude_regions.get(chrom, 0)
              if exclude_length < length:
                  out.append(chrom)
      return out
docs: Retrieve chromosomes to process on, avoiding extra skipped chromosomes.