private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+ string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
bool abort;
vector<string> outputNames, Groups;
GroupMap* groupMap;
+ map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+ //then the other files need to change the unique name in their file to match.
+ //only add the names that need to be changed to keep the map search quick
+
int readFasta();
+ int readShared();
int readName();
int readGroup();
void readAccnos();