public:
TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
- TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
+ TrimOligos(int,int, int, int, map<string, int>, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
+ TrimOligos(int,int, int, int, map<string, int>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
~TrimOligos();
int stripBarcode(Sequence&, int&);
int stripBarcode(Sequence&, QualityScores&, int&);
+
+ int stripRBarcode(Sequence&, int&);
+ int stripRBarcode(Sequence&, QualityScores&, int&);
int stripForward(Sequence&, int&);
int stripForward(Sequence&, QualityScores&, int&, bool);
int pdiffs, bdiffs, ldiffs, sdiffs;
map<string, int> barcodes;
+ map<string, int> rbarcodes;
map<string, int> primers;
vector<string> revPrimer;
vector<string> linker;