vector<string> setParameters();
string getCommandName() { return "sffinfo"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
string getDescription() { return "extract sequences reads from a .sff file"; }
int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
set<string> seqNames;
map<string, int> barcodes;
- map<string, int> rbarcodes;
map<string, int> primers;
vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
vector<vector<int> > numSplitReads;