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 {
20 TrimSeqsCommand(string);
27 bool stripBarcode(Sequence&, string&);
28 bool stripForward(Sequence&);
29 bool stripReverse(Sequence&);
30 bool cullLength(Sequence&);
31 bool cullHomoP(Sequence&);
32 bool cullAmbigs(Sequence&);
34 GlobalData* globaldata;
36 map<string, string> parameters;
37 map<string, string>::iterator it;
41 int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
42 vector<string> forPrimer, revPrimer;
43 map<string, string> barcodes;