vector<string> setParameters();
string getCommandName() { return "sff.multiple"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
string getDescription() { return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
int end;
linePair(int i, int j) : start(i), end(j) {}
};
-
+
+ string inputDir;
string filename, outputDir, flowOrder, lookupFileName, minDelta;
vector<string> outputNames;
bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;