//create reoriented primer and barcode pairs
map<int, oligosPair> rpairedPrimers, rpairedBarcodes;
for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
- cout << "primer " << (it->second).forward << '\t' << (it->second).reverse << '\t' << primerNameVector[it->first] << endl;
- cout << "rprimer " << trimOligos->reverseOligo((it->second).reverse) << '\t' << (trimOligos->reverseOligo((it->second).forward)) << endl;
- oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
+ oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
rpairedPrimers[it->first] = tempPair;
}
for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
- cout << "barcode " << (it->second).forward << '\t' << (it->second).reverse << '\t' << barcodeNameVector[it->first] << endl;
- cout << "rbarcode " << trimOligos->reverseOligo((it->second).reverse) << '\t' << (trimOligos->reverseOligo((it->second).forward)) << endl;
- oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
+ oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
rpairedBarcodes[it->first] = tempPair;
}
rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
}
oligosPair newPrimer(oligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
//check for repeat barcodes
string tempPair = oligo+roligo;
if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
}
- oligosPair newPair(oligo, reverseOligo(reverseBarcode));
+ reverseBarcode = reverseOligo(reverseBarcode);
+ oligosPair newPair(oligo, reverseBarcode);
if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }