int screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
int screenAlignReport(set<string>);
+ int screenQual(set<string>);
int driver(linePair*, string, string, string, set<string>&);
int createProcesses(string, string, string, set<string>&);
#endif
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
vector<string> outputNames;
vector<string> optimize;