string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
-
+ string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
+ string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
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;