uint Aligner::mapOnLeftEndExhaustive(const string &read, vector<uNumber>& path, const pair<kmer, uint>& overlap , uint errors){
string unitig, readLeft(read.substr(0,overlap.second));
vector<uNumber> path2keep;
if(readLeft.size()==0){return 0;}
auto rangeUnitigs(getEnd(overlap.first));
uint miniMiss(errors+1),miniMissIndice(9);
int offset(-2);
bool ended(false);
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;
offset=unitig.size()-readLeft.size()-k+1;
ended=true;
}
}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)));
vector<uNumber> possiblePath;
miss+=mapOnLeftEndExhaustive(read , possiblePath, {overlapNum,overlap.second-(unitig.size()-k+1)}, errors-miss);
if(miss<miniMiss){
path2keep=possiblePath;
miniMiss=miss;
miniMissIndice=i;
offset=-1;
ended=false;
}
}
}
}
if (miniMiss<=errors){
if(ended){
path.push_back(offset);
}else{
path.insert(path.end(), path2keep.begin(),path2keep.end());
}
path.push_back(rangeUnitigs[miniMissIndice].second);
}
return miniMiss;
}
uint Aligner::checkBeginExhaustive(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);
int offset(-2);
bool ended(false);
vector<uNumber> path2keep;
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<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<minMiss){
kmer overlapNum(str2num(unitig.substr(0,k-1)));
vector<uNumber> possiblePath;
miss+=mapOnLeftEndExhaustive(read, possiblePath, {overlapNum,overlap.second-(unitig.size()-k+1)},errors-miss);
if(miss<minMiss){
sucessML++;
minMiss=miss;
indiceMinMiss=i;
path2keep=possiblePath;
ended=false;
}
}
}
}
if(minMiss<=errors){
if(ended){
path.push_back(offset);
path.push_back(rangeUnitigs[indiceMinMiss].second);
}else{
path.insert(path.end(), path2keep.begin(), path2keep.end());
path.push_back(rangeUnitigs[indiceMinMiss].second);
}
}
return minMiss;
}
