1 #ifndef CHIMERACHECKCOMMAND_H
2 #define CHIMERACHECKCOMMAND_H
5 * chimeracheckcommand.h
8 * Created by westcott on 3/31/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
16 #include "chimeracheckrdp.h"
19 /***********************************************************/
21 class ChimeraCheckCommand : public Command {
23 ChimeraCheckCommand(string);
24 ChimeraCheckCommand();
25 ~ChimeraCheckCommand(){}
27 vector<string> setParameters();
28 string getCommandName() { return "chimera.check"; }
29 string getCommandCategory() { return "Sequence Processing"; }
30 string getHelpString();
33 void help() { m->mothurOut(getHelpString()); }
39 unsigned long int start;
40 unsigned long int end;
41 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
44 vector<int> processIDS; //processid
45 vector<linePair*> lines;
47 int driver(linePair*, string, string);
48 int createProcesses(string, string);
51 int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
55 string fastafile, templatefile, namefile, outputDir;
56 int processors, increment, ksize, numSeqs, templateSeqsLength;
58 vector<string> fastaFileNames;
59 vector<string> nameFileNames;
60 vector<string> outputNames;
63 /***********************************************************/