+ else{
+ //check for reverse match
+ if (alignment != NULL) { delete alignment; }
+
+ if (irbarcodes.size() > 0) { alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxRBarcodeLength+bdiffs+1)); }
+ else{ alignment = NULL; }
+
+ //can you find the barcode
+ minDiff = 1e6;
+ minCount = 1;
+ vector< vector<int> > minRGroup;
+ vector<int> minRPos;
+
+ for(map<string, vector<int> >::iterator it=irbarcodes.begin();it!=irbarcodes.end();it++){
+ string oligo = it->first;
+ //cout << "before = " << oligo << '\t' << rawRSequence.substr(0,oligo.length()+bdiffs) << endl;
+ if(rawRSequence.length() < maxRBarcodeLength){ //let's just assume that the barcodes are the same length
+ success = bdiffs + 10;
+ break;
+ }
+
+ //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
+ alignment->align(oligo, rawRSequence.substr(0,oligo.length()+bdiffs));
+ oligo = alignment->getSeqAAln();
+ string temp = alignment->getSeqBAln();
+
+ int alnLength = oligo.length();
+ for(int i=oligo.length()-1;i>=0;i--){ if(oligo[i] != '-'){ alnLength = i+1; break; } }
+ oligo = oligo.substr(0,alnLength);
+ temp = temp.substr(0,alnLength);
+ int numDiff = countDiffs(oligo, temp);
+ if (alnLength == 0) { numDiff = bdiffs + 100; }
+
+ //cout << "after = " << oligo << '\t' << temp << '\t' << numDiff << endl;
+ if(numDiff < minDiff){
+ minDiff = numDiff;
+ minCount = 1;
+ minRGroup.clear();
+ minRGroup.push_back(it->second);
+ int tempminRPos = 0;
+ minRPos.clear();
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ }else if(numDiff == minDiff){
+ int tempminRPos = 0;
+ for(int i=0;i<alnLength;i++){
+ if(temp[i] != '-'){
+ tempminRPos++;
+ }
+ }
+ minRPos.push_back(tempminRPos);
+ minRGroup.push_back(it->second);
+ }
+
+ }
+
+ /*cout << minDiff << '\t' << minCount << '\t' << endl;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minFGroup[i].size(); j++) { cout << minFGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;
+ for (int i = 0; i < minRGroup.size(); i++) {
+ cout << i << '\t';
+ for (int j = 0; j < minRGroup[i].size(); j++) { cout << minRGroup[i][j] << " "; }
+ cout << endl;
+ }
+ cout << endl;*/
+ if(minDiff > bdiffs) { success = minDiff; } //no good matches
+ else {
+ bool foundMatch = false;
+ vector<int> matches;
+ for (int i = 0; i < minFGroup.size(); i++) {
+ for (int j = 0; j < minFGroup[i].size(); j++) {
+ for (int k = 0; k < minRGroup.size(); k++) {
+ if (m->inUsersGroups(minFGroup[i][j], minRGroup[k])) { matches.push_back(minFGroup[i][j]); k+= minRGroup.size(); }
+ }
+ }
+ }
+
+ int fStart = 0;
+ int rStart = 0;
+ if (matches.size() == 1) {
+ foundMatch = true;
+ group = matches[0];
+ fStart = minFPos[0];
+ rStart = minRPos[0];
+ }
+
+ //we have an acceptable match for the forward and reverse, but do they match?
+ if (foundMatch) {
+ forwardSeq.setUnaligned(rawFSequence.substr(fStart));
+ reverseSeq.setUnaligned(rawRSequence.substr(rStart));
+ forwardQual.trimQScores(fStart, -1);
+ reverseQual.trimQScores(rStart, -1);
+ success = minDiff;
+ }else { success = bdiffs + 100; }
+ }