bool abort;
string fastaFile, oligoFile, qFileName;
- bool flip, allFiles;
+ bool flip, allFiles, qtrim;
int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage;
vector<string> forPrimer, revPrimer;
map<string, int> barcodes;