fixed some bugs

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b9b208493f2f6fea9a35055c448b65973ddc6a46..aaed841ed8012a274cb96c3153463b4c1b0a2bc0 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,17 +9,13 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "utilities.hpp"
 #include "fastamap.h"
 #include "globaldata.hpp"
 
-/* The deconvolute command reads a fasta file, finds the duplicate sequences and outputs a names file
+/* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
        containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */ 
 
-using namespace std;
 
 class DeconvoluteCommand : public Command {
 
@@ -32,8 +28,8 @@ private:
        GlobalData* globaldata;
        FastaMap* fastamap;
        ifstream in;
-       ofstream out;
-       string filename, outputFileName;
+       ofstream out, outFasta;
+       string filename, outputFileName, outFastafile;
 
 };