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"
18 /***********************************************************/
20 class ChimeraCheckCommand : public Command {
22 ChimeraCheckCommand(string);
23 ~ChimeraCheckCommand();
31 unsigned long int start;
33 linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
35 vector<int> processIDS; //processid
36 vector<linePair*> lines;
38 int driver(linePair*, string, string);
39 int createProcesses(string, string);
42 int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
46 string fastafile, templatefile, namefile, outputDir;
47 int processors, increment, ksize, numSeqs, templateSeqsLength;
49 vector<string> fastaFileNames;
50 vector<string> nameFileNames;
51 vector<string> outputNames;
55 /***********************************************************/