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;
+ int maxLength;
ofstream errorSummaryFile, errorSeqFile;
vector<string> outputNames;
map<string, vector<string> > outputTypes;
vector<Sequence> referenceSeqs;
vector<vector<int> > substitutionMatrix;
- int a,t,g,c,gap,n;
};
#endif