changed dups parameter to dereplicate in chimera.uchime.

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 7235a7b68ec569412bb97d1b98f076ff3b439bdb..d1fb1226236dc3842b9ace53536cf95a266f1d5e 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -16,6 +16,7 @@
 #include "rabundvector.hpp"
 #include "inputdata.h"
 #include "sequence.hpp"
+#include "counttable.h"
 
 
 class SubSampleCommand : public Command {
@@ -28,6 +29,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "sub.sample";  }
        string getCommandCategory()             { return "General";             }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
        string getDescription()         { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
@@ -37,13 +39,14 @@ public:
        
 private:       
        bool abort, pickedGroups, allLines, persample;
-       string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+       string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir;
        vector<string> Groups, outputNames;
        int size;
        vector<string> names;
        map<string, vector<string> > nameMap;
+    CountTable ct;
        
        int getSubSampleShared();
        int getSubSampleList();