1 #ifndef SUBSAMPLECOMMAND_H
2 #define SUBSAMPLECOMMAND_H
8 * Created by westcott on 10/27/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sharedrabundvector.h"
20 class SubSampleCommand : public Command {
23 SubSampleCommand(string);
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 GlobalData* globaldata;
37 vector<SharedRAbundVector*> lookup;
42 bool abort, allLines, pickedGroups;
43 set<string> labels; //holds labels to be used
44 string groups, label, outputDir;
45 vector<string> Groups, outputNames;
46 map<string, vector<string> > outputTypes;
48 int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
49 int getSubSampleShared(vector<SharedRAbundVector*>&, ofstream&);