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;
34 linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
36 vector<int> processIDS; //processid
37 vector<linePair*> lines;
39 int driver(linePair*, string, string);
40 int createProcesses(string, string);
43 int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
47 string fastafile, templatefile, namefile, outputDir;
48 int processors, increment, ksize, numSeqs, templateSeqsLength;
50 vector<string> fastaFileNames;
51 vector<string> nameFileNames;
52 vector<string> outputNames;
56 /***********************************************************/