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//
// mergeotuscommand.hpp
// Mothur
//
// Created by Sarah Westcott on 12/10/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef mergeotuscommand_hpp
#define mergeotuscommand_hpp
#include "command.hpp"
#include "phylotree.h"
#include "inputdata.h"
class MergeOTUsCommand : public Command {
public:
MergeOTUsCommand(string);
~MergeOTUsCommand();
vector<string> setParameters();
string getCommandName() { return "merge.otus"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Merge.otus"; }
string getDescription() { return "combine otus based on consensus taxonomy"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
string label, constaxfile, sharedfile, listfile, relabundfile;
int taxLevelCutoff;
vector<string> Groups, outputNames;
set<string> labels;
map<string, string> otuLabel2ConsTax;
map<string, int> otuLabel2ConsSize; //for use with list file, since list file only contains uniques
int mergeListOTUs(vector<TaxNode>&);
int mergeSharedOTUs(vector<TaxNode>&);
int mergeRelabundOTUs(vector<TaxNode>&);
int process(SharedRAbundVectors*&, ofstream&, bool&, vector<TaxNode>& nodes);
int process(ListVector*&, ofstream&, bool&, vector<TaxNode>& nodes);
int process(SharedRAbundFloatVectors*&, ofstream&, bool&, vector<TaxNode>& nodes);
};
#endif /* mergeotuscommand_hpp */
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