X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=e8ca96a6328ee56cf56ff1e9a1869107b359896f;hb=45b880733289694b2a23c9dc8a774aa626458f81;hp=c8dd4efb232b4e5c2ce0727c8d5badaf2433d6a9;hpb=85af0d7ce5839dfd39981811f149157c305dd31a;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index c8dd4ef..e8ca96a 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -60,7 +60,7 @@ private:
 	void printErrorHeader();
 	void printErrorData(Compare);
 	
-	string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
 	double threshold;
 	int numRefs;
 	ofstream errorSummaryFile, errorSeqFile;
@@ -68,6 +68,8 @@ private:
 	map<string, vector<string> > outputTypes;
 	
 	vector<Sequence> referenceSeqs;
+	vector<vector<int> > substitutionMatrix;
+	int a,t,g,c,gap,n;
 };
 
 #endif