uint Aligner::checkEndExhaustive(const string& read, pair<kmer, uint>& overlap, vector<uNumber>& path, uint errors){
string readLeft(read.substr(overlap.second+k-1)),unitig;
vector<uNumber> path2keep;
if(readLeft.empty()){
path.push_back(0);
return 0;
}
auto rangeUnitigs(getBegin(overlap.first));
uint minMiss(errors+1),indiceMinMiss(9);
bool ended(false);
int offset(-2);
if(partial & rangeUnitigs.empty()){
//if(!path.empty()){
return 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;
offset=readLeft.size()+k-1;
}
}else{
uint miss(missmatchNumber(unitig.substr(k-1),readLeft.substr(0,unitig.size()-k+1), errors));
if(miss<minMiss){
kmer overlapNum(str2num(unitig.substr(unitig.size()-k+1,k-1)));
vector<uNumber> possiblePath;
miss+=mapOnRightEndExhaustive(read, possiblePath, {overlapNum,overlap.second+(unitig.size()-k+1)},errors-miss);
if(miss<minMiss){
path2keep=possiblePath;
minMiss=miss;
indiceMinMiss=i;
ended=false;
}
}
}
}
if(minMiss<=errors){
if(ended){
path.push_back(rangeUnitigs[indiceMinMiss].second);
path.push_back(offset);
}else{
path.push_back(rangeUnitigs[indiceMinMiss].second);
path.insert(path.end(), path2keep.begin(),path2keep.end());
}
}
return minMiss;
}
uint Aligner::mapOnRightEndExhaustive(const string &read, vector<uNumber>& path, const pair<kmer, uint>& overlap , uint errors){
string unitig,readLeft(read.substr(overlap.second+k-1));
vector<uNumber> path2keep;
if(readLeft.empty()){path.push_back(0);return 0;}
auto rangeUnitigs(getBegin(overlap.first));
uint miniMiss(errors+1), miniMissIndice(9);
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()<= unitig.size()-k+1){
uint miss(missmatchNumber(unitig.substr(k-1,readLeft.size()), readLeft, errors));
if(miss<miniMiss){
miniMiss=miss;
miniMissIndice=i;
ended=true;
}
}else{
//case the read is big enough we want to recover a true overlap
uint miss(missmatchNumber(unitig.substr(k-1), readLeft.substr(0,unitig.size()-k+1), errors));
if(miss<miniMiss){
kmer overlapNum(str2num(unitig.substr(unitig.size()-k+1,k-1)));
vector<uNumber> possiblePath;
miss+=mapOnRightEndExhaustive(read , possiblePath, {overlapNum,overlap.second+(unitig.size()-k+1)}, errors-miss);
if(miss<miniMiss){
path2keep=possiblePath;
miniMiss=miss;
miniMissIndice=i;
ended=false;
}
}
}
}
if(miniMiss<=errors){
if(ended){
path.push_back(rangeUnitigs[miniMissIndice].second);
path.push_back(readLeft.size()+k-1);
}else{
path.push_back(rangeUnitigs[miniMissIndice].second);
path.insert(path.end(), path2keep.begin(),path2keep.end());
}
successMR++;
}
return miniMiss;
}
