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();
24 ~ChimeraSlayerCommand();
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
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&);
49 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
52 bool abort, realign, trim, trimera;
53 string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
54 int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
58 vector<string> outputNames;
59 map<string, vector<string> > outputTypes;
60 vector<string> fastaFileNames;
61 vector<string> nameFileNames;
65 /***********************************************************/