- bool oligos, flip;
- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
+ bool abort;
+ string fastaFile, oligoFile, qFileName;
+
+ bool flip, allFiles;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;