1 #ifndef CHIMERABELLEROPHONCOMMAND_H
2 #define CHIMERABELLEROPHONCOMMAND_H
5 * chimerabellerophoncommand.h
8 * Created by westcott on 4/1/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 /***********************************************************/
20 class ChimeraBellerophonCommand : public Command {
22 ChimeraBellerophonCommand(string);
23 ChimeraBellerophonCommand();
24 ~ChimeraBellerophonCommand();
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map< string, vector<string> > getOutputFiles() { return outputTypes; }
34 bool abort, filter, correction;
35 string fastafile, outputDir;
36 int processors, window, increment, numSeqs;
38 vector<string> outputNames;
39 map<string, vector<string> > outputTypes;
40 vector<string> fastaFileNames;
43 /***********************************************************/