removed make count from make.contigs

[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
index 9e58c064f1c8e0c1bf5a4356c028ba9a60afed80..2cab7be6fa870d763de76a559b4dfbb72823cfb6 100644 (file)
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -26,7 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "remove.rare";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
        string getDescription()         { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
 
@@ -35,7 +37,7 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+       string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
        int nseqs, allLines;
        bool abort, byGroup;
        vector<string> outputNames, Groups;