X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=c8dd4efb232b4e5c2ce0727c8d5badaf2433d6a9;hb=85af0d7ce5839dfd39981811f149157c305dd31a;hp=983383bdc3b6842db303685e2dd96f421e30d614;hpb=3247d888e7aafc4a65ec9062a94dfd166c2c5b1d;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 983383b..c8dd4ef 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -16,7 +16,7 @@
 
 struct Compare {
 	int AA, AT, AG, AC,	TA, TT, TG, TC,	GA, GT, GG, GC,	CA, CT, CG, CC,	NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
-	string refName, queryName;
+	string refName, queryName, sequence;
 	double errorRate;
 	int weight, matches, mismatches, total;
 	
@@ -35,6 +35,7 @@ struct Compare {
 		mismatches = 0;
 		total = 0;
 		errorRate = 1.0000;
+		sequence = "";
 	}
 };
 
@@ -59,10 +60,10 @@ private:
 	void printErrorHeader();
 	void printErrorData(Compare);
 	
-	string queryFileName, referenceFileName, namesFileName, errorFileName, outputDir;
+	string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
 	double threshold;
 	int numRefs;
-	ofstream errorFile;
+	ofstream errorSummaryFile, errorSeqFile;
 	vector<string> outputNames;
 	map<string, vector<string> > outputTypes;