collapse3col.cpp

/*    collapse3col: collapsebed but fast and only for 3 column bed
 *
 *    Copyright (C) 2018 Andrew D. Smith
 *
 *    Authors: Andrew D. Smith
 *
 *    This program 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.
 *
 *    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#include "OptionParser.hpp"
#include "smithlab_utils.hpp"
#include "smithlab_os.hpp"
#include "GenomicRegion.hpp"

using std::string;
using std::vector;
using std::endl;
using std::cerr;
using std::cin;
using std::cout;
using std::runtime_error;

int
main(int argc, const char **argv) {

  try {

    /****************** GET COMMAND LINE ARGUMENTS ***************************/
    OptionParser opt_parse(strip_path(argv[0]), "", "");
    vector<string> leftover_args;
    opt_parse.parse(argc, argv, leftover_args);
    if (opt_parse.help_requested()) {
      cerr << opt_parse.help_message() << endl;
      return EXIT_SUCCESS;
    }
    if (opt_parse.about_requested()) {
      cerr << opt_parse.about_message() << endl;
      return EXIT_SUCCESS;
    }
    if (opt_parse.option_missing()) {
      cerr << opt_parse.option_missing_message() << endl;
      return EXIT_SUCCESS;
    }
    if (!leftover_args.empty()) {
      cerr << opt_parse.help_message() << endl;
      return EXIT_SUCCESS;
    }
    /**********************************************************************/

    std::ios_base::sync_with_stdio(false);

    SimpleGenomicRegion curr;
    if (!(cin >> curr))
      throw runtime_error("could not read interval from file");

    SimpleGenomicRegion prev(curr);
    SimpleGenomicRegion gr;
    while (cin >> gr) {
      if (gr < prev)
        throw runtime_error("intervals not sorted:\n" +
                            gr.tostring() + "\n" +
                            prev.tostring());

      if (gr.overlaps(curr))
        curr.set_end(gr.get_end());
      else {
        cout << curr << '\n';
        curr = gr;
      }
      prev = gr;
    }
    cout << curr << '\n';
  }
  catch (std::runtime_error &e) {
    cerr << "ERROR:\t" << e.what() << endl;
    return EXIT_FAILURE;
  }
  catch (std::bad_alloc &ba) {
    cerr << "ERROR: could not allocate memory" << endl;
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}