#include "listvector.hpp"
#include "fastamap.h"
#include "groupmap.h"
+#include "counttable.h"
class BinSeqCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "bin.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
string getDescription() { return "maps sequences to otus"; }
void help() { m->mothurOut(getHelpString()); }
private:
-
+ CountTable ct;
ListVector* list;
InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
bool abort, allLines;
set<string> labels; //holds labels to be used
- string filename, fastafile, listfile, namesfile, groupfile, label, outputDir;
+ string filename, fastafile, listfile, namesfile, groupfile, countfile, label, outputDir;
ofstream out;
ifstream in, inNames;
vector<string> outputNames;