*** empty log message ***

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e8ca96a6328ee56cf56ff1e9a1869107b359896f..00b536771ca730945324a3674d2a34646cddf25d 100644 (file)
--- 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;