X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removerarecommand.h;h=6a9f2699c6d0a404403372e8ab081d11c9fa85d1;hp=2ab1272efbef88fdb008f903cf02a7d66ed3215a;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/removerarecommand.h b/removerarecommand.h
index 2ab1272..6a9f269 100644
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -26,14 +26,18 @@ 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"; }
+
 	
 	int execute(); 
 	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;
@@ -43,7 +47,7 @@ private:
 	int processRabund();
 	int processList();
 	int processShared();
-	int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+	int processLookup(vector<SharedRAbundVector*>&);
 	
 };