void simulate(char* modelF, char* resultsF) {
ModelType model(&refs);
ReadType read;
int sid;
model.read(modelF);
//calculate eel
calcExpectedEffectiveLengths<ModelType>(M, refs, model, eel);
//generate theta vector
ifstream fin(resultsF);
string line;
double tpm;
double denom = 0.0;
getline(fin, line); // read the first line, which is just column names
for (int i = 1; i <= M; i++) {
getline(fin, line);
size_t pos = 0;
for (int j = 0; j < OFFSITE; j++) pos = line.find_first_of('\t', pos) + 1;
size_t pos2 = line.find_first_of('\t', pos);
if (pos2 == string::npos) pos2 = line.length();
tpm = atof(line.substr(pos, pos2 - pos).c_str());
theta[i] = tpm * eel[i]; // during simulation, there is no check for effL < 0. The reason is for that case, eel[i] here = 0 and therefore no chance to sample from it
denom += theta[i];
}
assert(denom > EPSILON);
fin.close();
for (int i = 1; i <= M; i++) theta[i] = theta[i] / denom * (1.0 - theta[0]);
READ_INT_TYPE resimulation_count = 0;
//simulating...
model.startSimulation(sampler, theta);
for (READ_INT_TYPE i = 0; i < N; i++) {
while (!model.simulate(i, read, sid)) { ++resimulation_count; }
read.write(n_os, os);
++counts[sid];
if ((i + 1) % 1000000 == 0 && verbose) cout<<"GEN "<< i + 1<< endl;
}
model.finishSimulation();
cout<< "Total number of resimulation is "<< resimulation_count<< endl;
}
inline
bool ReadRegionData::read_exists(ReadType const& read) const {
return _read_regions.count(read.query_name()) > 0;
}
inline
bool ReadRegionData::read_exists(ReadType const& read) const {
return _read_regions.find(read->query_name()) != _read_regions.end();
}