-
- TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
+ TrimOligos* trimOligos = NULL;
+ int numBarcodes = pDataArray->barcodes.size();
+ if (pDataArray->pairedOligos) { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->pairedPrimers, pDataArray->pairedBarcodes); numBarcodes = pDataArray->pairedBarcodes.size(); pDataArray->numFPrimers = pDataArray->pairedPrimers.size(); }
+ else { trimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer); }
+
+ TrimOligos* rtrimOligos = NULL;
+ if (pDataArray->reorient) {
+ //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;
+ }
+ rtrimOligos = new TrimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
+ }