- string fastafile;
- bool oligos, flip;
- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
- vector<string> forPrimer, revPrimer;
- map<string, string> barcodes;
+ string fastaFile, oligoFile, qFileName, outputDir;
+
+ bool flip, allFiles, qtrim;
+ 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;
+ map<string, int> barcodes;
+ vector<string> groupVector;
+ map<string, int> primers;
+ map<string, int> combos;
+
+ vector<int> processIDS; //processid
+ vector<linePair*> lines;
+ vector<linePair*> qLines;
+
+ int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
+ int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
+ int setLines(string, vector<linePair*>&);
+