X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.h;h=735c97d1269848b94ac5a01926f93e08d1ccd5ef;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=a5b42751dfd74ea3eb1fc3dc4ccf9bfa5bb9822b;hpb=cc19310422f125d6628980bd1148e1e816792382;p=mothur.git

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index a5b4275..735c97d 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -28,9 +28,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.uchime";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code was donated to the public domain.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.uchime\n"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute();