private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
bool abort, dups;
vector<string> outputNames;
map<string, string> uniqueMap;
int readFasta();
+ int readFastq();
int readName();
int readGroup();
int readCount();