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#ifndef TRIMOLIGOS_H
#define TRIMOLIGOS_H
/*
* trimoligos.h
* Mothur
*
* Created by westcott on 9/1/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "mothurout.h"
#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 {
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<int, oligosPair>, map<int, oligosPair>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes
~TrimOligos();
int stripBarcode(Sequence&, int&);
int stripBarcode(Sequence&, QualityScores&, int&);
int stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
int stripBarcode(Sequence&, Sequence&, int&);
int stripForward(Sequence&, int&);
int stripForward(Sequence&, QualityScores&, int&, bool);
int stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
int stripForward(Sequence&, Sequence&, int&);
bool stripReverse(Sequence&);
bool stripReverse(Sequence&, QualityScores&);
bool stripLinker(Sequence&);
bool stripLinker(Sequence&, QualityScores&);
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;
vector<string> revPrimer;
vector<string> linker;
vector<string> spacer;
map<string, vector<int> > ifbarcodes;
map<string, vector<int> > ifprimers;
map<string, vector<int> > irbarcodes;
map<string, vector<int> > irprimers;
map<int, oligosPair> ipbarcodes;
map<int, oligosPair> ipprimers;
int maxFBarcodeLength, maxRBarcodeLength, maxFPrimerLength, maxRPrimerLength, maxLinkerLength, maxSpacerLength;
MothurOut* m;
bool compareDNASeq(string, string);
int countDiffs(string, string);
int stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
int stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
};
#endif
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