private:
GlobalData* globaldata;
- ReadOTUFile* read;
- InputData* input;
- string outputDir, sabundfile, rabundfile, listfile, format, path;
+ string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
bool abort, allLines;
set<string> labels;
vector<string> outputNames;
map< string, vector<string> > outputTypes;
+ vector<string> groups;
- string process(SAbundVector*);
- string createSummaryFile(string, string);
+ string process(SAbundVector*, string);
+ int createSummaryFile(string, string, ofstream&);
+ vector<string> parseSharedFile(string);
+ string combineSummmary(vector<string>&);
};
/****************************************************************************/