#include "sequence.hpp"
#include "qualityscores.h"
-struct oligosPair {
- string forward;
- string reverse;
-
- oligosPair() { forward = ""; reverse = ""; }
- oligosPair(string f, string r) : forward(f), reverse(r) {}
- ~oligosPair() {}
-};
class TrimOligos {
bool findReverse(Sequence&, int&, int&);
string reverseOligo(string);
- string getTrashCode() { return trashCode; }
-
private:
int pdiffs, bdiffs, ldiffs, sdiffs;
bool paired;
- string trashCode;
map<string, int> barcodes;
map<string, int> primers;
int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
+ int stripPairedBarcode(Sequence& seq, int& group);
+ int stripPairedPrimers(Sequence& seq, int& group);
+
};
#endif