public:
ChimeraCcodeCommand(string);
ChimeraCcodeCommand();
- ~ChimeraCcodeCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ChimeraCcodeCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.ccode"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+ string getDescription() { return "detect chimeric sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
- bool abort, filter;
+ bool abort, filter, save;
string fastafile, templatefile, outputDir, maskfile;
int processors, window, numwanted, numSeqs, templateSeqsLength;
Chimera* chimera;
vector<string> fastaFileNames;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
-
-
};
/***********************************************************/