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(){}
27 vector<string> setParameters();
28 string getCommandName() { return "chimera.check"; }
29 string getCommandCategory() { return "Sequence Processing"; }
31 string getHelpString();
32 string getOutputPattern(string);
33 string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
34 string getDescription() { return "detect chimeric sequences"; }
37 void help() { m->mothurOut(getHelpString()); }
43 unsigned long long start;
44 unsigned long long end;
45 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
48 vector<int> processIDS; //processid
49 vector<linePair*> lines;
51 int driver(linePair*, string, string);
52 int createProcesses(string, string);
55 int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
58 bool abort, svg, save;
59 string fastafile, templatefile, namefile, outputDir;
60 int processors, increment, ksize, numSeqs, templateSeqsLength;
62 vector<string> fastaFileNames;
63 vector<string> nameFileNames;
64 vector<string> outputNames;
67 /***********************************************************/