docs: def getIndex(reference):
      '''
      Find the reference folder using the location of the script file
      Create the index, test if successful
      '''
      if reference:
          reffas = reference
      else:
          parent_directory = path.dirname(path.abspath(path.dirname(__file__)))
          reffas = path.join(parent_directory, "reference/DNA_CS.fasta")
      if not path.isfile(reffas):
          logging.error("Could not find reference fasta for lambda genome.")
          sys.exit("Could not find reference fasta for lambda genome.")
      aligner = mp.Aligner(reffas, preset="map-ont")  # build index
      if not aligner:
          logging.error("Failed to load/build index")
          raise Exception("ERROR: failed to load/build index")
      return aligner