vector<string> outputNames;
string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
+
+ //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.
int readFasta();
int readName();
int readTax();
int readQual();
int compareAccnos();
+ int runSanityCheck();
+ int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
};