bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
+ int countDiffs(string, string);//, int, int&, int);
bool abort;
string fastaFile, oligoFile, qFileName, outputDir;
bool flip, allFiles, qtrim;
- int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, diffs;
+ int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, currentSeqsTdiffs;
vector<string> forPrimer, revPrimer, outputNames;
map<string, int> barcodes;
vector<string> groupVector;