uint Aligner::checkBeginGreedy(const string& read, pair<kmer, uint>& overlap, vector<uNumber>& path, uint errors){
if(overlap.second==0){path.push_back(0);return 0;}
string readLeft(read.substr(0,overlap.second)),unitig;
auto rangeUnitigs(getEnd(overlap.first));
uint minMiss(errors+1),indiceMinMiss(0);
bool ended(false);
int offset(0);
kmer nextOverlap(0);
for(uint i(0); i<rangeUnitigs.size(); ++i){
unitig=(rangeUnitigs[i].first);
if(unitig.size()-k+1>=readLeft.size()){
uint miss(missmatchNumber(unitig.substr(unitig.size()-readLeft.size()-k+1,readLeft.size()),readLeft, errors));
// if(miss==0){
// path.push_back(unitig.size()-readLeft.size()-k+1);
// path.push_back(rangeUnitigs[i].second);
// return 0;
// }
if(miss<minMiss){
minMiss=miss;
indiceMinMiss=i;
ended=true;
offset=unitig.size()-readLeft.size()-k+1;
}
}else{
uint miss(missmatchNumber(unitig.substr(0,unitig.size()-k+1), readLeft.substr(readLeft.size()+k-1-unitig.size()), errors));
// if(miss==0){
// minMiss+=mapOnLeftEndGreedy(read, path, {nextOverlap,overlap.second-(nextUnitig.size()-k+1)},errors);
// if(minMiss<=errors){
// path.push_back(rangeUnitigs[indiceMinMiss].second);
// sucessML++;
// }
// }
if(miss<minMiss){
kmer overlapNum(str2num(unitig.substr(0,k-1)));
if(miss<minMiss){
ended=false;
minMiss=miss;
indiceMinMiss=i;
nextOverlap=overlapNum;
}
}
}
}
if(minMiss<=errors){
if(ended){
path.push_back(offset);
path.push_back(rangeUnitigs[indiceMinMiss].second);
return minMiss;
}
minMiss+=mapOnLeftEndGreedy(read, path, {nextOverlap,overlap.second-(rangeUnitigs[indiceMinMiss].first.size()-k+1)},errors-minMiss);
if(minMiss<=errors){
path.push_back(rangeUnitigs[indiceMinMiss].second);
sucessML++;
}
}
return minMiss;
}
uint Aligner::mapOnRightEndGreedy(const string &read, vector<uNumber>& path, const pair<kmer, uint>& overlap , uint errors){
// cout<<"moreg"<<endl;
string unitig,readLeft(read.substr(overlap.second)),nextUnitig;
// auto rangeUnitigs(getBeginOpti(overlap.first,path.back()));
auto rangeUnitigs(getBegin(overlap.first));
uint miniMiss(errors+1), miniMissIndice(9);
bool ended(false);
// int offset(0);
kmer nextOverlap(0);
// cout<<"go"<<endl;
// for(uint i(0); i<rangeUnitigs2.size(); ++i){
// cout<<(rangeUnitigs2[i].first)<<endl;
// }
// cout<<"true"<<endl;
for(uint i(0); i<rangeUnitigs.size(); ++i){
unitig=(rangeUnitigs[i].first);
// bool stop(false);
// if(rangeUnitigs[i].first!=rangeUnitigs2[i].first){
// cout<<read<<endl;
// cout<<"lol2"<<endl;
// cout<<rangeUnitigs[i].first<<endl<<rangeUnitigs2[i].first<<endl;
// cout<<rangeUnitigs[i].second<<" "<<rangeUnitigs2[i].second<<endl;
// stop=true;
// }
// if(stop){cin.get();}
// cout<<unitig<<endl;
// cout<<rangeUnitigs[i].first<<endl;
//case the rest of the read is too small
if(readLeft.size()<=unitig.size()){
uint miss(missmatchNumber(unitig.substr(0,readLeft.size()), readLeft, errors));
if(miss<miniMiss){
miniMiss=miss;
miniMissIndice=i;
ended=true;
// offset=unitig.size()-readLeft.size()-k+1;
}
}else{
//case the read is big enough we want to recover a true overlap
uint miss(missmatchNumber(unitig, read.substr(overlap.second,unitig.size()), errors));
if(miss<miniMiss){
if(miss<miniMiss){
kmer overlapNum(str2num(unitig.substr(unitig.size()-k+1,k-1)));
miniMiss=miss;
miniMissIndice=i;
nextUnitig=unitig;
nextOverlap=overlapNum;
}
}
}
}
// cout<<"end"<<endl;
if(miniMiss<=errors){
path.push_back(rangeUnitigs[miniMissIndice].second);
if (ended){return miniMiss;}
miniMiss+=mapOnRightEndGreedy(read , path, {nextOverlap,overlap.second+(nextUnitig.size()-k+1)}, errors-miniMiss);
}
return miniMiss;
}
uint Aligner::mapOnLeftEndGreedy(const string &read, vector<uNumber>& path, const pair<kmer, uint>& overlap , uint errors){
// if(overlap.second==0){path.push_back(0);return 0;}
string unitig,readLeft(read.substr(0,overlap.second)),nextUnitig;
auto rangeUnitigs(getEnd(overlap.first));
uint miniMiss(errors+1),miniMissIndice(9);
bool ended(false);
int offset(0);
kmer nextOverlap(0);
for(uint i(0); i<rangeUnitigs.size(); ++i){
unitig=(rangeUnitigs[i].first);
//case the rest of the read is too small
if(readLeft.size()+k-1 <= unitig.size()){
uint miss(missmatchNumber(unitig.substr(unitig.size()-readLeft.size()-k+1,readLeft.size()), readLeft, errors));
if(miss<miniMiss){
miniMiss=miss;
miniMissIndice=i;
ended=true;
offset=unitig.size()-readLeft.size()-k+1;
}
}else{
//case the read is big enough we want to recover a true overlap
uint miss(missmatchNumber(unitig.substr(0,unitig.size()-k+1), readLeft.substr(readLeft.size()-(unitig.size()-k+1)), errors));
if(miss<miniMiss){
kmer overlapNum(str2num(unitig.substr(0,k-1)));
if(miss<miniMiss){
ended=false;
miniMiss=miss;
miniMissIndice=i;
nextUnitig=unitig;
nextOverlap=overlapNum;
}
}
}
}
if (miniMiss<=errors){
if(ended){
path.push_back(offset);
path.push_back(rangeUnitigs[miniMissIndice].second);
return miniMiss;
}
miniMiss+=mapOnLeftEndGreedy(read , path, {nextOverlap,overlap.second-(nextUnitig.size()-k+1)}, errors-miniMiss);
path.push_back(rangeUnitigs[miniMissIndice].second);
}
return miniMiss;
}
uint Aligner::checkEndGreedy(const string& read, pair<kmer, uint>& overlap, vector<uNumber>& path, uint errors){
string readLeft(read.substr(overlap.second+k-1)),unitig,nextUnitig;
if(readLeft.size()<=k-1){return 0;}
auto rangeUnitigs(getBegin(overlap.first));
uint minMiss(errors+1),indiceMinMiss(9);
bool ended(false);
kmer nextOverlap(0);
for(uint i(0); i<rangeUnitigs.size(); ++i){
unitig=(rangeUnitigs[i].first);
if(unitig.size()-k+1>=readLeft.size()){
uint miss(missmatchNumber(unitig.substr(k-1,readLeft.size()),readLeft, errors));
if(miss<minMiss){
minMiss=miss;
indiceMinMiss=i;
ended=true;
}
}else{
uint miss(missmatchNumber(unitig.substr(k-1),readLeft.substr(0,unitig.size()-k+1), errors));
if(miss<minMiss){
if(miss<minMiss){
kmer overlapNum(str2num(unitig.substr(unitig.size()-k+1,k-1)));
minMiss=miss;
indiceMinMiss=i;
nextOverlap=overlapNum;
nextUnitig=unitig;
}
}
}
}
if(minMiss<=errors){
path.push_back(rangeUnitigs[indiceMinMiss].second);
if(ended){
return minMiss;
}
minMiss+=mapOnRightEndGreedy(read, path, {nextOverlap,overlap.second+(nextUnitig.size()-k+1)},errors-minMiss);
if(minMiss<=errors){
successMR++;
}
}
return minMiss;
}
