bug fix to seq.error

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 983383bdc3b6842db303685e2dd96f421e30d614..05afe6054ce2cc49f2d5f763d57b78a4ff01b475 100644 (file)
--- 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 = "";
        }
 };
 
@@ -57,16 +58,22 @@ private:
        map<string,int> getWeights();
        Compare getErrors(Sequence, Sequence);
        void printErrorHeader();
-       void printErrorData(Compare);
-       
-       string queryFileName, referenceFileName, namesFileName, errorFileName, 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 errorFile;
+       ofstream errorSummaryFile, errorSeqFile;
        vector<string> outputNames;
        map<string, vector<string> > outputTypes;
        
        vector<Sequence> referenceSeqs;
+       vector<vector<int> > substitutionMatrix;
 };
 
 #endif