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();
29 string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
33 void help() { m->mothurOut(getHelpString()); }
38 unsigned long int start;
39 unsigned long int end;
40 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
43 vector<int> processIDS; //processid
44 vector<linePair*> lines;
46 int driver(linePair*, string, string, string, string);
47 int createProcesses(string, string, string, string);
48 int divideInHalf(Sequence, string&, string&);
49 map<string, int> sortFastaFile(string, string);
52 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
55 bool abort, realign, trim, trimera;
56 string fastafile, templatefile, outputDir, search, namefile;
57 int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
61 vector<string> outputNames;
62 vector<string> fastaFileNames;
63 vector<string> nameFileNames;
67 /***********************************************************/