vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
string flowFileName, oligoFileName, outputDir;
-
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;