- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+ 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
+ string accnosfile, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;