class TrimOligos {
public:
- TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
+ 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 stripBarcode(Sequence&, int&);
int stripBarcode(Sequence&, QualityScores&, int&);
int stripForward(Sequence&, int&);
- int stripForward(Sequence&, QualityScores&, int&);
+ int stripForward(Sequence&, QualityScores&, int&, bool);
bool stripReverse(Sequence&);
bool stripReverse(Sequence&, QualityScores&);
+
+ bool stripLinker(Sequence&);
+ bool stripLinker(Sequence&, QualityScores&);
+
+ bool stripSpacer(Sequence&);
+ bool stripSpacer(Sequence&, QualityScores&);
private:
- int pdiffs, bdiffs;
+ int pdiffs, bdiffs, ldiffs, sdiffs;
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;
+ vector<string> linker;
+ vector<string> spacer;
MothurOut* m;