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#ifndef CHIMERAPINTAILCOMMAND_H
#define CHIMERAPINTAILCOMMAND_H
/*
* chimerapintailcommand.h
* Mothur
*
* Created by westcott on 4/1/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "mothurchimera.h"
/***********************************************************/
class ChimeraPintailCommand : public Command {
public:
ChimeraPintailCommand(string);
~ChimeraPintailCommand(){}
vector<string> setParameters();
string getCommandName() { return "chimera.pintail"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int checkChimeras();
int lookForShortcutFiles(string baseName);
bool abort, filter, save, removeChimeras;
string fastafile, templatefile, consfile, quanfile, maskfile, inputDir;
int window, increment, numSeqs, templateSeqsLength;
vector<string> outputNames;
};
/***********************************************************/
#endif
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