added N for trimOligos change

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e7c97e152d718b8944b0e004b32398dd1f210e99..9f400b328c93aa8d03bd176283b3df17974dc0f4 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -24,8 +24,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "seq.error";                           }
        string getCommandCategory()             { return "Sequence Processing";         }
+       
        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"; }
 
        
@@ -90,7 +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;