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"
17 /***********************************************************/
19 class ChimeraSlayerCommand : public Command {
21 ChimeraSlayerCommand(string);
22 ChimeraSlayerCommand();
23 ~ChimeraSlayerCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "chimera.slayer"; }
27 string getCommandCategory() { return "Sequence Processing"; }
28 string getHelpString();
31 void help() { m->mothurOut(getHelpString()); }
36 unsigned long int start;
37 unsigned long int end;
38 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
41 vector<int> processIDS; //processid
42 vector<linePair*> lines;
44 int driver(linePair*, string, string, string, string);
45 int createProcesses(string, string, string, string);
46 int divideInHalf(Sequence, string&, string&);
47 map<string, int> sortFastaFile(string, string);
50 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
53 bool abort, realign, trim, trimera;
54 string fastafile, templatefile, outputDir, search, namefile;
55 int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
59 vector<string> outputNames;
60 vector<string> fastaFileNames;
61 vector<string> nameFileNames;
65 /***********************************************************/