read_uid_mapping.cpp

/*
 * Copyright 2017-2018, Florian Breitwieser
 *
 * This file is part of the KrakenUniq taxonomic sequence classification system.
 *
 * KrakenUniq is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * KrakenUniq is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with Kraken.  If not, see <http://www.gnu.org/licenses/>.
 */

#include "uid_mapping.hpp"
#include "kraken_headers.hpp"
#include "quickfile.hpp"
#include <unordered_map>
#include <algorithm>

using namespace std;
using namespace kraken;

int main(int argc, char **argv) {
  if (argc < 2) {
    std::cerr << "Usage: read_uid_mapping <uid mappingfile> [<uid>]"
        "The file is supposed to have lines terminated by '\n'.it.second"
         << std::endl;
    return 1;
  }
  char *filename = argv[1];
  kraken::QuickFile UID_to_TaxID_map_file;
  UID_to_TaxID_map_file.open_file(filename);

  char* fptr = UID_to_TaxID_map_file.ptr();
  if (argc == 2) {
    vector< vector <uint32_t> > UIDs_to_taxids;
    uint32_t UID = 1;
    size_t int_size = sizeof(UID);
    size_t i = 0;
    for (size_t pos = 0; pos < UID_to_TaxID_map_file.size(); pos += 2*int_size) {
      uint32_t* taxid_ptr  = (uint32_t*)(fptr+pos);
      uint32_t* parent_uid = (uint32_t*)(fptr+pos+int_size);
      //UIDs_to_taxids.push_back( { UIDs_to_taxids[] } );
      //pos += int_size;
      cout << ++i << '\t' << *taxid_ptr << '\t' << *parent_uid << endl;
    }
  } else {
    //unordered_map<uint32_t, vector<uint32_t> > UID_to_TaxID_map;
    for (int i=2; i <argc; ++i) {
      uint32_t UID = atol(argv[i]);
      vector<uint32_t> taxids = get_taxids_for_uid(UID, fptr);
      cout << UID << '\t';
      for (auto it = taxids.begin(); it != taxids.end(); ++it) {
        cout << *it << ' ';
      }
      cout << endl;
    }
  }

  return 0;
}