Pre-index a generated local reference sequence with cortex_var and stampy.

def _index_local_ref(fasta_file, cortex_dir, stampy_dir, kmers):
    """Pre-index a generated local reference sequence with cortex_var and stampy.
    """
    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]}