- int totalBarcodeCount, matchBarcodeCount; // to be removed
- int totalFPrimerCount, matchFPrimerCount; // to be removed
- int totalRPrimerCount, matchRPrimerCount; // to be removed
+ bool abort;
+ string fastaFile, oligoFile, qFileName, outputDir;
+
+ bool flip, allFiles, qtrim;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
+ vector<string> forPrimer, revPrimer, outputNames;
+ map<string, int> barcodes;
+ vector<string> groupVector;
+
+ vector<int> processIDS; //processid
+ vector<linePair*> lines;
+ vector<linePair*> qLines;
+
+ int driverCreateTrim(string, string, string, string, string, vector<string>, linePair*, linePair*);
+ int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
+ int setLines(string, vector<linePair*>&);