code: def _matches_contigs(in_file, contigs, checked_file):
      
      tocheck_contigs = 2
      if utils.file_exists(checked_file):
          with open(checked_file) as in_handle:
              return in_handle.read().strip() == "match"
      else:
          with utils.open_gzipsafe(in_file) as in_handle:
              to_check = set([])
              for line in in_handle:
                  if not line.startswith("#"):
                      to_check.add(line.split()[0])
                  if len(to_check) >= tocheck_contigs:
                      break
          with open(checked_file, "w") as out_handle:
              if any([c not in contigs for c in to_check]):
                  out_handle.write("different")
                  return False
              else:
                  out_handle.write("match")
                  return True
docs: Check if the contigs in the input file match the defined contigs in the reference genome.