vector<string> setParameters();
string getCommandName() { return "trim.flows"; }
- string getCommandCategory() { return "Hidden"; }
+ string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
- string getCitation() { return "no citation"; }
+ string getCitation() { return "http://www.mothur.org/wiki/Trim.flows"; }
string getDescription() { return "trim.flows"; }
bool allFiles;
int processors;
int numFPrimers, numRPrimers;
- int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+ int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
int numFlows;
float signal, noise;
bool fasta;
map<string, int> barcodes;
map<string, int> primers;
vector<string> revPrimer;
+ vector<string> linker;
+ vector<string> spacer;
vector<string> primerNameVector; //needed here?
vector<string> barcodeNameVector; //needed here?
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
-typedef struct trimFlowData {
+struct trimFlowData {
string flowFileName;
string trimFlowFileName;
string scrapFlowFileName;