*
*/
-#include "mothur.h"
+
#include "command.hpp"
class ParseSFFCommand : public Command {
public:
ParseSFFCommand(string);
+ ParseSFFCommand();
~ParseSFFCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
map<string, int> barcodes;
vector<string> groupVector;
vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
// string stripSeqQual(string, int, int);
// string stripQualQual(string, int, int);