void getOligos(vector<string>&);
bool stripQualThreshold(Sequence&, ifstream&);
bool cullQualAverage(Sequence&, ifstream&);
- bool stripBarcode(Sequence&, int&);
- bool stripForward(Sequence&);
+ int stripBarcode(Sequence&, int&);
+ int stripForward(Sequence&);
bool stripReverse(Sequence&);
bool cullLength(Sequence&);
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;
+ 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;