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);
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
32 string fastafile, outputDir, keep;
33 bool abort, countGaps, Short;
35 vector<string> outputNames;
36 map<string, vector<string> > outputTypes;
38 string getChopped(Sequence);