changes while testing

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e7c97e152d718b8944b0e004b32398dd1f210e99..aac17b6979910ebc733be840eb37ec720ecc1105 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "referencedb.h"
+#include "counttable.h"
 
 
 class SeqErrorCommand : public Command {
@@ -24,8 +25,10 @@ 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"; }
 
        
@@ -88,9 +91,9 @@ private:
        int driver(string, string, string, string, string, string, linePair, linePair, linePair);
        int createProcesses(string, string, string, string, string, string);
 
-       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
+       string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
        double threshold;
-       bool ignoreChimeras, save;
+       bool ignoreChimeras, save, aligned;
        int numRefs, processors;
        int maxLength, totalBases, totalMatches;
        //ofstream errorSummaryFile, errorSeqFile;