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> 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;