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//
// vsearchfileparser.h
// Mothur
//
// Created by Sarah Westcott on 10/13/15.
// Copyright (c) 2015 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__vsearchfileparser__
#define __Mothur__vsearchfileparser__
#include "mothurout.h"
#include "uniqueseqscommand.h"
#include "sequence.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
/**************************************************************************************************/
class VsearchFileParser {
#ifdef UNIT_TEST
friend class TestVsearchFileParser;
#endif
public:
VsearchFileParser();
VsearchFileParser(string f); //fastafile
VsearchFileParser(string f, string n, string format); //fastafile, name or count file, format("name" or "count")
~VsearchFileParser(){}
string getVsearchFile(); //creates vsearch formatted file. degapped, abundance appended, and sorted.
string getCountFile(); //returns count filename. If no names or count file is given, then a count file is generated.
ListVector createListFile(string uc, int numbins, string label, map<string, int>& counts); //takes vsearch output and creates listvector
int getNumBins(string logfile);
void setFastaFile(string f) { fastafile = f; }
private:
MothurOut* m;
map<string, string> nameMap;
map<string, int> counts;
string fastafile, namefile, countfile, format;
string getNamesFile(string& inputFile);
string createVsearchFasta(string);
string removeAbundances(string seqName);
};
/**************************************************************************************************/
#endif /* defined(__Mothur__vsearchfileparser__) */
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