INNER CODE UNIT · C++

entries

fbreitwieser/krakenuniq · src/db_sort.cpp:83

  uint64_t entries = 1ull << (nt * 2);
  uint64_t key_len = kdb.get_key_len();
  uint64_t val_len = kdb.get_val_len();
  uint64_t pair_size = key_len + val_len;
  char pair[pair_size];

  ifstream input_file(Input_DB_filename.c_str(), std::ifstream::binary);
  input_file.seekg(kdb.header_size(), ios_base::beg);

  // Create a copy of the offsets array for use as insertion positions
  vector<uint64_t> pos(offsets, offsets + entries);
  for (uint64_t i = 0; i < kdb.get_key_ct(); i++) {
    input_file.read(pair, pair_size);
    uint64_t kmer = 0;
    memcpy(&kmer, pair, key_len);
    uint64_t b_key = kdb.bin_key(kmer, nt);
    char *pair_pos = data + pair_size * pos[b_key]++;
    // Copy pair into correct bin (but not final position)

View source record →