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//
// mergesfffilecommand.h
// Mothur
//
// Created by Sarah Westcott on 1/31/14.
// Copyright (c) 2014 Schloss Lab. All rights reserved.
//
#ifndef Mothur_mergesfffilecommand_h
#define Mothur_mergesfffilecommand_h
#include "command.hpp"
#include "sffheader.hpp"
#include "sffread.hpp"
/**********************************************************/
class MergeSfffilesCommand : public Command {
public:
MergeSfffilesCommand(string);
~MergeSfffilesCommand();
vector<string> setParameters();
string getCommandName() { return "merge.sfffiles"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/merge.sfffiles"; }
string getDescription() { return "merge individual sfffiles into a single .sff file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string sffFilename, file, currentFileName;
vector<string> filenames, outputNames;
bool abort, keyTrim;
int numTotalReads, allFilesnumFlowReads, allFileskeyLength;
string outputFile, outputFileHeader;
vector<SffCommonHeader*> commonHeaders;
//extract sff file functions
int mergeSffInfo(string, ofstream&);
void adjustCommonHeader();
void readFile();
};
/**********************************************************/
#endif
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