vector<string> outputNames;
string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
-
+ map<string, string> uniqueMap;
//for debug
map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.