1 #ifndef CHIMERAUCHIMECOMMAND_H
2 #define CHIMERAUCHIMECOMMAND_H
6 * chimerauchimecommand.h
9 * Created by westcott on 5/13/11.
10 * Copyright 2011 Schloss Lab. All rights reserved.
15 #include "command.hpp"
17 /***********************************************************/
19 class ChimeraUchimeCommand : public Command {
21 ChimeraUchimeCommand(string);
22 ChimeraUchimeCommand();
23 ~ChimeraUchimeCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "chimera.uchime"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getHelpString();
29 string getCitation() { return "http://drive5.com/uchime/ \nhttp://www.mothur.org/wiki/Chimera.uchime"; }
33 void help() { m->mothurOut(getHelpString()); }
36 vector<int> processIDS; //processid
37 int driver(string, string, string);
38 int createProcesses(string, string, string);
41 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
45 string fastafile, templatefile, outputDir, namefile;
48 vector<string> outputNames;
49 vector<string> fastaFileNames;
50 vector<string> nameFileNames;
54 /***********************************************************/