1 #ifndef CHIMERASLAYERCOMMAND_H
2 #define CHIMERASLAYERCOMMAND_H
5 * chimeraslayercommand.h
8 * Created by westcott on 3/31/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
18 /***********************************************************/
20 class ChimeraSlayerCommand : public Command {
22 ChimeraSlayerCommand(string);
23 ~ChimeraSlayerCommand();
31 unsigned long int start;
32 unsigned long int end;
33 linePair(unsigned long int i, unsigned long int j) : start(i), end(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, outputDir, search;
48 int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
52 vector<string> outputNames;
53 vector<string> fastaFileNames;
57 /***********************************************************/