code: def _index_local_ref(fasta_file, cortex_dir, stampy_dir, kmers):
      
      base_out = os.path.splitext(fasta_file)[0]
      cindexes = []
      for kmer in kmers:
          out_file = "{0}.k{1}.ctx".format(base_out, kmer)
          if not file_exists(out_file):
              file_list = "{0}.se_list".format(base_out)
              with open(file_list, "w") as out_handle:
                  out_handle.write(fasta_file + "\n")
              subprocess.check_call([_get_cortex_binary(kmer, cortex_dir),
                                     "--kmer_size", str(kmer), "--mem_height", "17",
                                     "--se_list", file_list, "--format", "FASTA",
                                     "--max_read_len", "30000",
  			           "--sample_id", base_out,
                                     "--dump_binary", out_file])
          cindexes.append(out_file)
      if not file_exists("{0}.stidx".format(base_out)):
          subprocess.check_call([os.path.join(stampy_dir, "stampy.py"), "-G",
                                 base_out, fasta_file])
          subprocess.check_call([os.path.join(stampy_dir, "stampy.py"), "-g",
                                 base_out, "-H", base_out])
      return {"stampy": base_out,
              "cortex": cindexes,
              "fasta": [fasta_file]}
docs: Pre-index a generated local reference sequence with cortex_var and stampy.