* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
+
+ /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
#include "command.hpp"
#include "globaldata.hpp"
#include "sparsematrix.hpp"
#include "listvector.hpp"
#include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
#include "fastamap.h"
SparseMatrix* matrix;
ListVector* list;
ListVector* listOfNames;
- ReadMatrix* read;
+ ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
string filename, fastafile, namesfile;