InputData* input;
Command* shared;
GroupMap* groupMap;
- string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format;
+ string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+ vector<string> Groups;
bool abort, allLines;
set<string> labels; //holds labels to be used