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#ifndef Mothur_sffmultiplecommand_h
#define Mothur_sffmultiplecommand_h
//
// sffmultiplecommand.h
// Mothur
//
// Created by Sarah Westcott on 8/14/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "sffinfocommand.h"
#include "seqsummarycommand.h"
#include "trimflowscommand.h"
#include "shhhercommand.h"
#include "trimseqscommand.h"
class SffMultipleCommand : public Command {
public:
SffMultipleCommand(string);
~SffMultipleCommand(){}
vector<string> setParameters();
string getCommandName() { return "sff.multiple"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
string getDescription() { return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string inputDir;
string filename, flowOrder, lookupFileName, minDelta;
vector<string> outputNames;
bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;
int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
int processors, maxIters, largeSize;
float signal, noise, cutoff, sigma;
int keepFirst, removeLast, maxAmbig;
int readFile(vector<string>& sffFiles, vector<string>& oligosFiles);
long long createProcesses(vector<string> sffFiles, vector<string> oligosFiles, string, string, string);
};
#endif
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