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
25 int stripBarcode(Sequence&, int&);
26 int stripBarcode(Sequence&, QualityScores&, int&);
28 int stripForward(Sequence&, int&);
29 int stripForward(Sequence&, QualityScores&, int&);
31 bool stripReverse(Sequence&);
32 bool stripReverse(Sequence&, QualityScores&);
38 map<string, int> barcodes;
39 map<string, int> primers;
40 vector<string> revPrimer;
44 bool compareDNASeq(string, string);
45 int countDiffs(string, string);