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"; }
vector<unsigned long long> getFlowFileBreaks();
int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >);
int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-
+ string reverseOligo(string);
+
vector<string> outputNames;
set<string> filesToRemove;
string flowFileName, oligoFileName, outputDir;
-
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;