assembler.cpp

#include "assembler.hpp"

void Assembler::run() {
  cerr << "Assembler is brokwn. Need to fix it.." << endl;
  //   auto c = Configuration::getInstance();
  //   int num_batches = c->aggregate_batches;
  //   int tau = -1; // c->cutoff;

  // #pragma omp parallel for num_threads(c->threads)
  //   for (int j = 0; j < num_batches; j++) {
  //     string s_j = std::to_string(j);
  //     string inpath = c->workdir + "/solution_batch_" + s_j + ".sfs";
  //     string outpath = c->workdir + "/solution_batch_" + s_j +
  //     ".assembled.sfs"; ofstream outf(outpath); map<string, vector<SFS>> SFSs
  //     = parse_sfsfile(inpath, tau);
  //     // cout << SFSs.size() << "SFS in total." << endl ;
  //     for (map<string, vector<SFS>>::iterator it = SFSs.begin(); it !=
  //     SFSs.end();
  //          ++it) {
  //       string ridx = it->first;
  //       vector<SFS> sfs = it->second;
  //       vector<SFS> assembled_sfs = assemble(sfs);
  //       bool is_first = true;
  //       for (const SFS &sfs : assembled_sfs) {
  //         outf << (is_first ? ridx : "*") << "\t"
  //              << "\t" << sfs.s << "\t" << sfs.l << "\t" << sfs.c << endl;
  //         is_first = false;
  //       }
  //     }
  //     outf.close();
  //   }
}

vector<SFS> Assembler::assemble(vector<SFS> &sfs) {
  vector<SFS> assembled_sfs;
  sort(sfs.begin(), sfs.end());
  size_t i = 0;
  while (i < sfs.size()) {
    size_t j;
    for (j = i + 1; j < sfs.size(); ++j) {
      if (sfs[j - 1].qs + sfs[j - 1].l <= sfs[j].qs) {
        // non-overlapping
        uint l = sfs[j - 1].qs + sfs[j - 1].l - sfs[i].qs;
        assembled_sfs.push_back(SFS(sfs[i].qname, sfs[i].qs, l, sfs[i].htag));
        i = j;
        break;
      }
    }
    if (j == sfs.size()) {
      uint l = sfs[j - 1].qs + sfs[j - 1].l - sfs[i].qs;
      assembled_sfs.push_back(SFS(sfs[i].qname, sfs[i].qs, l, sfs[i].htag));
      i = j;
    }
  }
  return assembled_sfs;
}