1 #ifndef METASTATSCOMMAND_H
2 #define METASTATSCOMMAND_H
8 * Created by westcott on 9/16/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "sharedrabundvector.h"
17 class MetaStatsCommand : public Command {
20 MetaStatsCommand(string);
22 ~MetaStatsCommand() {}
24 vector<string> setParameters();
25 string getCommandName() { return "metastats"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
27 string getHelpString();
28 string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
29 string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; }
32 void help() { m->mothurOut(getHelpString()); }
38 linePair(int i, int j) : start(i), num(j) {}
40 vector<linePair> lines;
44 vector<SharedRAbundVector*> lookup;
46 bool abort, allLines, pickedGroups;
47 set<string> labels; //holds labels to be used
48 string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
49 vector<string> Groups, outputNames, Sets;
50 vector< vector<string> > namesOfGroupCombos;
51 int iters, processors;
54 int process(vector<SharedRAbundVector*>&);
55 int driver(int, int, vector<SharedRAbundVector*>&);