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#ifndef REMOVESEQSCOMMAND_H
#define REMOVESEQSCOMMAND_H
/*
* removeseqscommand.h
* Mothur
*
* Created by Sarah Westcott on 7/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
class RemoveSeqsCommand : public Command {
public:
RemoveSeqsCommand(string);
RemoveSeqsCommand();
~RemoveSeqsCommand(){}
vector<string> setParameters();
string getCommandName() { return "remove.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
set<string> names;
string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
vector<string> outputNames;
map<string, string> uniqueMap;
int readFasta();
int readFastq();
int readName();
int readGroup();
int readCount();
int readAlign();
int readList();
int readTax();
int readQual();
};
#endif
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