vector<string> setParameters();
string getCommandName() { return "list.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
string getDescription() { return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
private:
vector<string> names, outputNames;
- string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
+ string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
bool abort;
int readFasta();
int readAlign();
int readList();
int readTax();
+ int readCount();
};