X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=9f400b328c93aa8d03bd176283b3df17974dc0f4;hb=0a9b5ee954b60abbd24c797cece23fb4a487cc8a;hp=660544fff2982a325c325932b3972d9b3451f3c4;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 660544f..9f400b3 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -24,9 +24,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "seq.error";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
 	string getDescription()		{ return "seq.error"; }
 
 	
@@ -91,7 +92,7 @@ private:
 
 	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
 	double threshold;
-	bool ignoreChimeras, save;
+	bool ignoreChimeras, save, aligned;
 	int numRefs, processors;
 	int maxLength, totalBases, totalMatches;
 	//ofstream errorSummaryFile, errorSeqFile;