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::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::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;
}
