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;
- string outputDir, fastaQFile;
- bool abort;
+ string outputDir, fastaQFile, format;
+ bool abort, fasta, qual;
vector<int> convertQual(string);
+ vector<char> convertTable;
};
#endif