vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
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 screenNameGroupFile(set<string>);
int screenGroupFile(set<string>);
+ int screenCountFile(set<string>);
int screenAlignReport(set<string>);
int screenQual(set<string>);
int screenTaxonomy(set<string>);
#endif
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
- int readNames();
int getSummary(vector<unsigned long long>&);
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);