int main(int argc, char** argv) {
std::cout << std::endl;
char* ref = NULL;
// Important NOT invert (init requires argument to be parsed)
parseArguments(argc,argv);
initSimulator();
size_t N = Options::opts.N;
size_t m = Options::opts.m;
size_t M = Options::opts.M;
size_t Nbar = N - m + 1;
double pe = Options::opts.pe;
std::cout << std::endl;
std::cout << "\t\t+++++ Starting simulation +++++ \n\n";
std::cout << "* Reference generation... ";
ref = new char[N];
generateIIDGenome(N,ref);
std::string s(ref);
std::cout << "[OK]" << std::endl;
std::cout << "* Read generation... ";
std::priority_queue<Read> reads;
generateOfflineReads(s, reads);
std::cout << "[OK]" << std::endl;
std::cout << "* Processing reads... ";
Read r1 = reads.top();
reads.pop();
while(!reads.empty()) {
Read r2 = reads.top();
reads.pop();
size_t s = m - (r2.j - r1.j);
evaluateChainRelation(r1, r2, s);
int dh = -1;
if (s <= m) {
dh = prefixSuffixHammingDistance(r2.r, r1.r, s);
} else {
addNonOverlapRecord(r2.j - r1.j - m);
}
r1 = r2;
}
std::cout << "[OK]" << std::endl;
std::cout << "* Cleaning... ";
delete[] ref;
std::cout << "\n\n";
// printChainMatrix();
//printNonOverlapDistribution();
printFalsePositiveMatrix();
clearSimulator();
std::cout << "[OK]" << std::endl;
std::cout << std::endl;
return 0;
}
void ExplorerPane::clear()
{
clearMetadata();
clearErrors();
clearSimulator();
}
