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//
// makefilecommand.h
// Mothur
//
// Created by Sarah Westcott on 6/24/15.
// Copyright (c) 2015 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__makefilecommand__
#define __Mothur__makefilecommand__
#include "command.hpp"
class MakeFileCommand : public Command {
public:
MakeFileCommand(string);
~MakeFileCommand(){}
vector<string> setParameters();
string getCommandName() { return "make.file"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Make.file"; }
string getDescription() { return "creates a file file containing fastq filenames"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string inputDir, typeFile, prefix, delim;
vector<string> outputNames;
int numCols;
bool abort;
vector< vector<string> > prepareOutputs(vector< vector<string> > paired);
vector< vector<string> > prepareOutputs(vector<string> files);
vector<string> denoiseGroupNames(vector<string> files);
vector<string> createDefaultGroupNames(vector<string> files);
int fillAccnosFile(string tempFile);
vector< vector<string> > pairFiles(vector<string> files, vector<string>& singles);
void createFastqGzFile(vector<string>);
void createFastaFile(vector<string>);
};
#endif /* defined(__Mothur__makefilecommand__) */
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