private:
set<string> names;
vector<string> outputNames, listOfTaxons;
- string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+ string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
bool abort, dups;
int readFasta();
int readName();
int readGroup();
+ int readCount();
int readAlign();
int readList();
int readTax();