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#ifndef CHOPSEQSCOMMAND_H
#define CHOPSEQSCOMMAND_H
/*
* chopseqscommand.h
* Mothur
*
* Created by westcott on 5/10/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
#include "qualityscores.h"
#include "writer.h"
#include "fastqread.h"
class ChopSeqsCommand : public Command {
public:
ChopSeqsCommand(string);
~ChopSeqsCommand(){};
vector<string> setParameters();
string getCommandName() { return "chop.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
string getDescription() { return "trim sequence length"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string fastafile, fastqfile, keep, namefile, groupfile, countfile, qualfile, format;
bool abort, countGaps, Short, keepN;
int numbases, processors;
vector<string> outputNames;
bool runChopFasta(string&);
bool runChopFastq(string&);
bool getFastqChopped(FastqRead&);
bool createProcesses(string, string, string, string);
int processQual(string, string);
};
#endif
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