vector<uNumber> Aligner::alignReadGreedyCache(const string& read, bool& overlapFound, uint errors, bool rc){
auto listOverlap(getListOverlapCache(read));
if(listOverlap.empty()){++noOverlapRead;++readNumber;return {};}
overlaps+=listOverlap.size();
overlapFound=true;
for(uint start(0); start<=min(tryNumber-1,(uint)listOverlap.size()-1); ++start){
vector<uNumber> pathBegin;
uint errorBegin(checkBeginGreedyCache(read,listOverlap[start],pathBegin,errors));
if(errorBegin<=errors){
for(int end((int)listOverlap.size()-1); end>=max((int)start,(int)listOverlap.size()-(int)tryNumber); --end){
vector<uNumber> pathEnd;
uint errorsEnd(checkEndGreedyCache(read,listOverlap[end],pathEnd,errors-errorBegin));
if(errorsEnd+errorBegin<=errors){
vector<uNumber> pathCover;
bool ended(false);
uint errorCover(coverGreedyCache(read,listOverlap,start,end,pathCover,errors-errorsEnd-errorBegin,ended));
if(errorCover<=errors-errorsEnd-errorBegin){
++alignedRead;
++readNumber;
pathBegin.insert(pathBegin.end(), pathCover.begin(),pathCover.end());
if (!ended){pathBegin.insert(pathBegin.end(), pathEnd.begin(),pathEnd.end());}
return pathBegin;
}
}
}
}
}
//TODO TEST this
//if(!rc){return alignReadGreedy(reverseComplements(read), overlapFound,errors, true);}
++notAligned;
++readNumber;
return {};
}
vector<uNumber> Aligner::alignReadGreedy(const string& read, bool& overlapFound, uint errors, bool r){
vector<pair<kmer,uint>> listOverlap(getNOverlap(read,tryNumber));
if(listOverlap.empty()){++noOverlapRead;++readNumber;return {};}
overlapFound=true;
vector<uNumber> pathBegin,pathEnd;
for(uint start(0); start<(uint)listOverlap.size(); ++start){
pathBegin={};
uint errorBegin(checkBeginGreedy(read,listOverlap[start],pathBegin,errors));
if(errorBegin<=errors){
pathEnd={};
uint errorsEnd(checkEndGreedy(read,listOverlap[start],pathEnd,errors-errorBegin));
if(errorsEnd+errorBegin<=errors){
alignedRead++;
readNumber++;
pathBegin.insert(pathBegin.end(), pathEnd.begin(),pathEnd.end());
return pathBegin;
}
}
}
//TODO TEST this
//if(!rc){return alignReadGreedy(reverseComplements(read), overlapFound,errors, true);}
notAligned++;
readNumber++;
return {};
}
vector<uNumber> Aligner::alignReadExhaustive(const string& read, bool& overlapFound, uint errors){
vector<pair<kmer,uint>> listOverlap(getListOverlap(read));
if(listOverlap.empty()){++noOverlapRead;++readNumber;return {};}
overlaps+=listOverlap.size();
overlapFound=true;
vector<uNumber> pathBegin,pathEnd;
for(uint start(0); start<(uint)listOverlap.size(); ++start){
pathBegin={};
uint errorBegin(checkBeginExhaustive(read,listOverlap[start],pathBegin,errors));
if(errorBegin<=errors){
pathEnd={};
uint errorsEnd(checkEndExhaustive(read,listOverlap[start],pathEnd,errors-errorBegin));
if(errorsEnd+errorBegin<=errors){
alignedRead++;
readNumber++;
pathBegin.insert(pathBegin.end(), pathEnd.begin(),pathEnd.end());
return pathBegin;
}
}
}
notAligned++;
readNumber++;
return {};
}
