- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
- bool abort;
+ 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.