code: def check_bed_contigs(in_file, data):
      
      if not dd.get_ref_file(data):
          return
      contigs = set([])
      with utils.open_gzipsafe(in_file) as in_handle:
          for line in in_handle:
              if not line.startswith(("#", "track", "browser", "@")) and line.strip():
                  contigs.add(line.split()[0])
      ref_contigs = set([x.name for x in ref.file_contigs(dd.get_ref_file(data))])
      if contigs and len(contigs - ref_contigs) / float(len(contigs)) > 0.25:
          raise ValueError("Contigs in BED file %s not in reference genome:\n %s\n"
                           % (in_file, list(contigs - ref_contigs)) +
                           "This is typically due to chr1 versus 1 differences in BED file and reference.")
docs: Ensure BED file contigs match the reference genome.