1 #ifndef TRIMSEQSCOMMAND_H
2 #define TRIMSEQSCOMMAND_H
8 * Created by Pat Schloss on 6/6/09.
9 * Copyright 2009 Patrick D. Schloss. All rights reserved.
14 #include "command.hpp"
15 #include "globaldata.hpp"
16 #include "sequence.hpp"
18 class TrimSeqsCommand : public Command {
26 bool stripBarcode(Sequence&, string&);
27 bool stripForward(Sequence&);
28 bool stripReverse(Sequence&);
29 bool cullLength(Sequence&);
30 bool cullHomoP(Sequence&);
31 bool cullAmbigs(Sequence&);
33 GlobalData* globaldata;
36 int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
37 vector<string> forPrimer, revPrimer;
38 map<string, string> barcodes;