1 #ifndef CHOPSEQSCOMMAND_H
2 #define CHOPSEQSCOMMAND_H
8 * Created by westcott on 5/10/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "sequence.hpp"
17 class ChopSeqsCommand : public Command {
21 ChopSeqsCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "chop.seqs"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getHelpString();
31 void help() { m->mothurOut(getHelpString()); }
34 string fastafile, outputDir, keep;
35 bool abort, countGaps, Short;
37 vector<string> outputNames;
39 string getChopped(Sequence);