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//
// renameseqscommand.h
// Mothur
//
// Created by SarahsWork on 5/28/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_renameseqscommand_h
#define Mothur_renameseqscommand_h
#include "command.hpp"
#include "filefile.hpp"
class RenameSeqsCommand : public Command {
#ifdef UNIT_TEST
friend class TestRenameSeqsCommand;
#endif
public:
RenameSeqsCommand(string);
~RenameSeqsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "rename.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Rename.seqs"; }
string getDescription() { return "rename sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string fastaFile, fastqfile, listfile, nameFile, groupfile, placement, delim, countfile, qualfile, contigsfile, fileFile, mapFile, taxfile, groupName;
vector<string> outputNames;
bool abort, ignoreNew, gz;
map<string, string> nameMap;
void readQual(map<string, string>&);
void readTax(map<string, string>&);
void readContigs(map<string, string>&);
void readList(map<string, string>&);
void readFasta(map<string, string>&);
string readFastq(map<string, string>&);
int processFile();
int readMapFile(map<string, string>&);
vector< vector<string> > readFiles(vector<string>&, bool&);
void processNameGroupCountFiles(map<string, string>&, map<string, string>&);
};
#endif
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