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>, map<string, int>, vector<string>, vector<string>, vector<string>); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, rbarcodes, revPrimers, linker, spacer
24 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
27 int stripBarcode(Sequence&, int&);
28 int stripBarcode(Sequence&, QualityScores&, int&);
30 int stripRBarcode(Sequence&, int&);
31 int stripRBarcode(Sequence&, QualityScores&, int&);
33 int stripForward(Sequence&, int&);
34 int stripForward(Sequence&, QualityScores&, int&, bool);
36 bool stripReverse(Sequence&);
37 bool stripReverse(Sequence&, QualityScores&);
39 bool stripLinker(Sequence&);
40 bool stripLinker(Sequence&, QualityScores&);
42 bool stripSpacer(Sequence&);
43 bool stripSpacer(Sequence&, QualityScores&);
47 int pdiffs, bdiffs, ldiffs, sdiffs;
49 map<string, int> barcodes;
50 map<string, int> rbarcodes;
51 map<string, int> primers;
52 vector<string> revPrimer;
53 vector<string> linker;
54 vector<string> spacer;
58 bool compareDNASeq(string, string);
59 int countDiffs(string, string);