bool flip, allFiles, qtrim;
int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
- vector<string> forPrimer, revPrimer;
+ vector<string> forPrimer, revPrimer, outputNames;
map<string, int> barcodes;
vector<string> groupVector;
};