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