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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 "mothurout.h"
#include "sequence.hpp"
#include "qualityscores.h"
class TrimOligos {
#ifdef UNIT_TEST
friend class TestTrimOligos;
TrimOligos() { m = MothurOut::getInstance(); }
#endif
public:
TrimOligos(int,int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, rpdiffs, 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>, bool); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
~TrimOligos(){}
//codes : 10 means sequence shorter than barcode, 100 means multiple matches, MOTHURMAX no matches, 0 found match.
//[0] = forward for paired, [1] = code for forward, [2] = reverse for paired, [3] = code for reverse
//[0] = forward for single, [1] = code for forward
vector<int> stripBarcode(Sequence&, int&);
vector<int> stripBarcode(Sequence&, QualityScores&, int&);
vector<int> stripBarcode(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
vector<int> stripBarcode(Sequence&, Sequence&, int&);
vector<int> stripIndexBarcode(Sequence& forwardSeq, Sequence& reverseSeq, int& group);
vector<int> stripForward(Sequence&, int&);
vector<int> stripForward(Sequence&, QualityScores&, int&, bool);
vector<int> stripForward(Sequence&, Sequence&, QualityScores&, QualityScores&, int&);
vector<int> stripForward(Sequence&, Sequence&, int&);
vector<int> stripReverse(Sequence&);
vector<int> stripReverse(Sequence&, QualityScores&);
int stripLinker(Sequence&);
int stripLinker(Sequence&, QualityScores&);
int stripSpacer(Sequence&);
int stripSpacer(Sequence&, QualityScores&);
//seq, primerStart, primerEnd
vector<int> findForward(Sequence&, int&, int&);
vector<int> findReverse(Sequence&, int&, int&);
string reverseOligo(string);
string getCodeValue(int, int);
protected:
int pdiffs, bdiffs, ldiffs, sdiffs, rdiffs;
bool paired, hasIndex;
Utils util;
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);
vector<int> stripPairedBarcode(Sequence& seq, QualityScores& qual, int& group);
vector<int> stripPairedPrimers(Sequence& seq, QualityScores& qual, int& group, bool);
vector<int> stripPairedBarcode(Sequence& seq, int& group);
vector<int> stripPairedPrimers(Sequence& seq, int& group);
int preProcess(int,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
int preProcess(int p, int b, int l, int s, map<int, oligosPair> pr, map<int, oligosPair> br, bool hi);
};
#endif
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