added ignore option to oligos files for make.contigs, trim.seqs, trim.flows

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 660544fff2982a325c325932b3972d9b3451f3c4..6c7af2cc5a3977db356ed0806d5e4cff48e701ce 100644 (file)
--- 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"; }