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();
25 ~ChimeraCheckCommand();
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 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);
46 int createProcesses(string, string);
49 int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
53 string fastafile, templatefile, namefile, outputDir;
54 int processors, increment, ksize, numSeqs, templateSeqsLength;
56 vector<string> fastaFileNames;
57 vector<string> nameFileNames;
58 vector<string> outputNames;
59 map<string, vector<string> > outputTypes;
63 /***********************************************************/