8 * Created by westcott on 9/1/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "mothurout.h"
15 #include "sequence.hpp"
16 #include "qualityscores.h"
22 TrimOligos(int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
23 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
26 int stripBarcode(Sequence&, int&);
27 int stripBarcode(Sequence&, QualityScores&, int&);
29 int stripForward(Sequence&, int&);
30 int stripForward(Sequence&, QualityScores&, int&, bool);
32 bool stripReverse(Sequence&);
33 bool stripReverse(Sequence&, QualityScores&);
35 bool stripLinker(Sequence&);
36 bool stripLinker(Sequence&, QualityScores&);
38 bool stripSpacer(Sequence&);
39 bool stripSpacer(Sequence&, QualityScores&);
43 int pdiffs, bdiffs, ldiffs, sdiffs;
45 map<string, int> barcodes;
46 map<string, int> primers;
47 vector<string> revPrimer;
48 vector<string> linker;
49 vector<string> spacer;
53 bool compareDNASeq(string, string);
54 int countDiffs(string, string);