code: def _maybe_limit_chromosomes(data):
      
      std_chroms = []
      prob_chroms = []
      noalt_calling = "noalt_calling" in dd.get_tools_on(data) or "altcontigs" in dd.get_exclude_regions(data)
      for contig in ref.file_contigs(dd.get_ref_file(data)):
          if contig.name.find(":") > 0 or (noalt_calling and not chromhacks.is_nonalt(contig.name)):
              prob_chroms.append(contig.name)
          else:
              std_chroms.append(contig.name)
      if len(prob_chroms) > 0:
          return std_chroms
      else:
          return []
docs: Potentially limit chromosomes to avoid problematically named HLA contigs.
  
      HLAs have ':' characters in them which confuse downstream processing. If
      we have no problematic chromosomes we don't limit anything.