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();
32 unsigned long int start;
33 unsigned long int end;
34 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
37 vector<int> processIDS; //processid
38 vector<linePair*> lines;
40 int driver(linePair*, string, string);
41 int createProcesses(string, string);
44 int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
48 string fastafile, templatefile, namefile, outputDir;
49 int processors, increment, ksize, numSeqs, templateSeqsLength;
51 vector<string> fastaFileNames;
52 vector<string> nameFileNames;
53 vector<string> outputNames;
57 /***********************************************************/