public:
ParseFastaQCommand(string);
ParseFastaQCommand();
- ~ParseFastaQCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ParseFastaQCommand() {}
+ vector<string> setParameters();
+ string getCommandName() { return "parse.fastq"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+ string getDescription() { return "reads a fastq file and creates a fasta and quality file"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
- string outputDir, fastaQFile;
- bool abort;
+ string outputDir, fastaQFile, format;
+ bool abort, fasta, qual;
vector<int> convertQual(string);
+ vector<char> convertTable;
};
#endif