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(){}
26 vector<string> setParameters();
27 string getCommandName() { return "chimera.bellerophon"; }
28 string getCommandCategory() { return "Sequence Processing"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
33 string getDescription() { return "detect chimeric sequences"; }
36 void help() { m->mothurOut(getHelpString()); }
41 bool abort, filter, correction;
42 string fastafile, outputDir;
43 int processors, window, increment, numSeqs;
45 vector<string> outputNames;
46 vector<string> fastaFileNames;
49 /***********************************************************/