- TrimOligos trim(pDataArray->pdiffs, 0, pDataArray->primers, faked, pDataArray->revPrimer);
+ set<int> locations; //locations = beginning locations
+
+ Oligos oligos(pDataArray->oligosfile);
+ int numFPrimers, numRPrimers;
+ map<string, int> primers;
+ map<string, int> barcodes; //not used
+ vector<string> revPrimer;
+ if (oligos.hasPairedBarcodes()) {
+ numFPrimers = oligos.getPairedPrimers().size();
+ map<int, oligosPair> primerPairs = oligos.getPairedPrimers();
+ for (map<int, oligosPair>::iterator it = primerPairs.begin(); it != primerPairs.end(); it++) {
+ primers[(it->second).forward] = it->first;
+ revPrimer.push_back((it->second).reverse);
+ }
+ }else {
+ numFPrimers = oligos.getPrimers().size();
+ primers = oligos.getPrimers();
+ revPrimer = oligos.getReversePrimers();
+ }
+ numRPrimers = oligos.getReversePrimers().size();
+
+ TrimOligos trim(pDataArray->pdiffs, 0, primers, barcodes, revPrimer);