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#ifndef TRIMFLOWSCOMMAND_H
#define TRIMFLOWSCOMMAND_H
/*
* trimflowscommand.h
* Mothur
*
* Created by Pat Schloss on 12/22/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
#include "flowdata.h"
#include "groupmap.h"
#include "trimoligos.h"
#include "oligos.h"
#include "splitgroupscommand.h"
class TrimFlowsCommand : public Command {
public:
TrimFlowsCommand(string);
~TrimFlowsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
set<string> filesToRemove;
int numFPrimers, numRPrimers, numBarcodes, processors, numFlows, comboStarts;
int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
float signal, noise;
bool fasta, pairedOligos, reorient, allFiles, abort, createGroup;
string flowOrder, flowFileName, oligoFileName;
map<int, oligosPair> pairedBarcodes;
map<int, oligosPair> pairedPrimers;
map<string, int> barcodes;
map<string, int> primers;
vector<string> linker;
vector<string> spacer;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
vector<string> revPrimer;
map<string, string> groupMap;
vector<double> getFlowFileBreaks();
int createProcessesCreateTrim(string, string, string, string);
int getOligos();
};
#endif
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