- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, diffs;
- vector<string> forPrimer, revPrimer, outputNames;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+ int qWindowSize, qWindowStep;
+ double qRollAverage, qThreshold, qWindowAverage, qAverage;
+ vector<string> revPrimer, outputNames;
+ set<string> filesToRemove;