X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=00b536771ca730945324a3674d2a34646cddf25d;hb=fa08e82ec2dd48f73d051c210dad54a403308949;hp=e8ca96a6328ee56cf56ff1e9a1869107b359896f;hpb=0adea182fc7adb2d83492ac2c065fb30e0054e41;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e8ca96a..00b5367 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -58,10 +58,15 @@ private:
 	map<string,int> getWeights();
 	Compare getErrors(Sequence, Sequence);
 	void printErrorHeader();
-	void printErrorData(Compare);
-	
-	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+	void printErrorData(Compare, int);
+	void printSubMatrix();
+	void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
+	void printErrorQuality(map<char, vector<int> >);
+	void printQualityFR(vector<vector<int> >, vector<vector<int> >);
+
+	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
 	double threshold;
+	bool ignoreChimeras;
 	int numRefs;
 	ofstream errorSummaryFile, errorSeqFile;
 	vector<string> outputNames;