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();
26 ~ChimeraPintailCommand();
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
37 unsigned long int start;
38 unsigned long int end;
39 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
42 vector<int> processIDS; //processid
43 vector<linePair*> lines;
45 int driver(linePair*, string, string, string);
46 int createProcesses(string, string, string);
49 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
53 string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
54 int processors, window, increment, numSeqs, templateSeqsLength;
56 vector<string> outputNames;
57 map<string, vector<string> > outputTypes;
58 vector<string> fastaFileNames;
63 /***********************************************************/