bool stripSpacer(Sequence&);
bool stripSpacer(Sequence&, QualityScores&);
-
+
+ //seq, primerStart, primerEnd
+ bool findForward(Sequence&, int&, int&);
+ bool findReverse(Sequence&, int&, int&);
+
+ string reverseOligo(string);
private:
int pdiffs, bdiffs, ldiffs, sdiffs;
+ bool paired;
map<string, int> barcodes;
map<string, int> primers;
MothurOut* m;
bool compareDNASeq(string, string);
- int countDiffs(string, string);
+ int countDiffs(string, string);
+
+ int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
+ int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
};
#endif