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#ifndef Mothur_pcrseqscommand_h
#define Mothur_pcrseqscommand_h
//
// pcrseqscommand.h
// Mothur
//
// Created by Sarah Westcott on 3/14/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "sequence.hpp"
#include "trimoligos.h"
#include "alignment.hpp"
#include "needlemanoverlap.hpp"
#include "counttable.h"
#include "oligos.h"
#include "removeseqscommand.h"
class PcrSeqsCommand : public Command {
public:
PcrSeqsCommand(string);
~PcrSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "pcr.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
string getDescription() { return "pcr.seqs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, keepprimer, keepdots, fileAligned, pairedOligos, reorient;
string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, nomatch;
int start, end, processors, length, pdiffs, rdiffs;
vector<string> outputNames;
int writeAccnos(set<string>, string);
Sequence readEcoli();
long long createProcesses(string, string, string, set<string>&);
int adjustDots(string goodFasta, map<string, vector<int> > locations, int pstart, int pend, bool, bool);
};
/**************************************************************************************************/
#endif
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