X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqerrorcommand.h;h=aac17b6979910ebc733be840eb37ec720ecc1105;hp=660544fff2982a325c325932b3972d9b3451f3c4;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 660544f..aac17b6 100644
--- 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 {
@@ -24,9 +25,10 @@ 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"; }
 
 	
@@ -89,9 +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;