- //create reoriented primer and barcode pairs
- map<int, oligosPair> rpairedPrimers, rpairedBarcodes;
- for (map<int, oligosPair>::iterator it = pDataArray->pairedPrimers.begin(); it != pDataArray->pairedPrimers.end(); it++) {
- oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
- rpairedPrimers[it->first] = tempPair;
- }
- for (map<int, oligosPair>::iterator it = pDataArray->pairedBarcodes.begin(); it != pDataArray->pairedBarcodes.end(); it++) {
- oligosPair tempPair(trimOligos->reverseOligo((it->second).reverse), (trimOligos->reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
- rpairedBarcodes[it->first] = tempPair;
- }
-
- int index = rpairedBarcodes.size();
- for (map<string, int>::iterator it = pDataArray->barcodes.begin(); it != pDataArray->barcodes.end(); it++) {
- oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
- rpairedBarcodes[index] = tempPair; index++;
- }
-
- index = rpairedPrimers.size();
- for (map<string, int>::iterator it = pDataArray->primers.begin(); it != pDataArray->primers.end(); it++) {
- oligosPair tempPair("", trimOligos->reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
- rpairedPrimers[index] = tempPair; index++;
- }
-
- rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();