1 #ifndef CHIMERAPINTAILCOMMAND_H
2 #define CHIMERAPINTAILCOMMAND_H
5 * chimerapintailcommand.h
8 * Created by westcott on 4/1/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 /***********************************************************/
20 class ChimeraPintailCommand : public Command {
24 ChimeraPintailCommand(string);
25 ~ChimeraPintailCommand();
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, string);
40 int createProcesses(string, string, string);
43 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
47 string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
48 int processors, window, increment, numSeqs, templateSeqsLength;
50 vector<string> outputNames;
51 vector<string> fastaFileNames;
56 /***********************************************************/