void Aligner::alignPartGreedy(){
vector<pair<string,string>> multiread;
vector<uNumber> path;
string read,header;
bool overlapFound(false);
while(!readFile.eof()){
readMutex.lock();
{
getReads(multiread,10000);
}
readMutex.unlock();
for(uint i(0);i<multiread.size();++i){
overlapFound=false;
header=multiread[i].first;
read=multiread[i].second;
if(pathOption){
path=alignReadGreedyPath(read,overlapFound,errorsMax,false);
}else{
path=alignReadGreedy(read,overlapFound,errorsMax,false);
}
if(path.size()!=0){
// string lol(recoverPath(path,2*read.size()));
// if(lol!=read){
// lol=reverseComplements(lol);
// if(lol!=read){
// cin.get();
// }
// }
pathMutex.lock();
{
pathFile<<header<<endl;
printPath(path,&pathFile);
}
pathMutex.unlock();
}else{
if(!overlapFound){
noOverlapMutex.lock();
{
noOverlapFile<<header<<endl<<read<<endl;
//~ notMappedFile<<read<<endl;
}
noOverlapMutex.unlock();
}else{
notMappedMutex.lock();
{
notMappedFile<<header<<endl<<read<<endl;
//~ notMappedFile<<read<<endl;
}
notMappedMutex.unlock();
}
}
}
if(iter++%10==0){
cout<<"Read : "<<readNumber<<endl;
cout<<"No Overlap : "<<noOverlapRead<<" Percent : "<<(100*float(noOverlapRead))/readNumber<<endl;
cout<<"Got Overlap : "<<alignedRead+notAligned<<" Percent : "<<(100*float(alignedRead+notAligned))/readNumber<<endl;
cout<<"Overlap and Aligned : "<<alignedRead<<" Percent : "<<(100*float(alignedRead))/(alignedRead+notAligned)<<endl;
cout<<"Overlap but no aligne: "<<notAligned<<" Percent : "<<(100*float(notAligned))/(alignedRead+notAligned)<<endl;
auto end=chrono::system_clock::now();auto waitedFor=end-startChrono;
cout<<"Reads/seconds : "<<readNumber/(chrono::duration_cast<chrono::seconds>(waitedFor).count()+1)<<endl;
// cout<<"Overlap per reads : "<<(overlaps)/(alignedRead+notAligned)<<endl;
cout<<endl;
}
}
}
void Aligner::alignPartGreedy(){
vector<pair<string,string>> multiread;
vector<uNumber> path;
string read,header,corrected;
bool overlapFound(false);
while(!readFile.eof()){
readMutex.lock();
{
getReads(multiread,10000);
}
readMutex.unlock();
for(uint i(0);i<multiread.size();++i){
overlapFound=false;
header=multiread[i].first;
read=multiread[i].second;
if(pathOption){
path=alignReadGreedyPath(read,overlapFound,errorsMax,false);
}else{
path=alignReadGreedy(read,overlapFound,errorsMax,false);
}
if(path.size()!=0){
if(correctionMode){
//if(true){
corrected=(recoverPath(path,read.size()));
// pathFile<<header<<'\n';
// pathFile<<corrected<<'\n';
header+='\n'+corrected+'\n';
pathMutex.lock();
{
fwrite((header).c_str(), sizeof(char), header.size(), pathFilef);
}
pathMutex.unlock();
}else{
// pathFile<<header<<'\n';
header+='\n'+printPath(path);;
pathMutex.lock();
{
fwrite((header).c_str(), sizeof(char), header.size(), pathFilef);
}
pathMutex.unlock();
}
}else{
if(false){
noOverlapMutex.lock();
{
noOverlapFile<<header<<'\n'<<read<<'\n';
}
noOverlapMutex.unlock();
}else{
header+='\n'+read+'\n';
notMappedMutex.lock();
{
// notMappedFile<<header<<'\n'<<read<<'\n';
fwrite(header.c_str(), sizeof(char), header.size(), notMappedFilef);
// notMappedFile<<readNumber<<'\n';
// cout<<header<<'\n'<<read<<'\n';
}
notMappedMutex.unlock();
}
}
}
// if(iter++%10==0){
// cout<<"Read : "<<readNumber<<endl;
// cout<<"No Overlap : "<<noOverlapRead<<" Percent : "<<(100*float(noOverlapRead))/readNumber<<endl;
// cout<<"Got Overlap : "<<alignedRead+notAligned<<" Percent : "<<(100*float(alignedRead+notAligned))/readNumber<<endl;
// cout<<"Overlap and Aligned : "<<alignedRead<<" Percent : "<<(100*float(alignedRead))/(alignedRead+notAligned)<<endl;
// cout<<"Overlap but no aligne: "<<notAligned<<" Percent : "<<(100*float(notAligned))/(alignedRead+notAligned)<<endl;
// auto end=chrono::system_clock::now();auto waitedFor=end-startChrono;
// cout<<"Reads/seconds : "<<readNumber/(chrono::duration_cast<chrono::seconds>(waitedFor).count()+1)<<endl;
// // cout<<"Overlap per reads : "<<(overlaps)/(alignedRead+notAligned)<<endl;
// cout<<endl;
// }
}
}