void printErrorHeader();
void printErrorData(Compare);
- string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+ string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
double threshold;
int numRefs;
ofstream errorSummaryFile, errorSeqFile;
map<string, vector<string> > outputTypes;
vector<Sequence> referenceSeqs;
+ vector<vector<int> > substitutionMatrix;
+ int a,t,g,c,gap,n;
};
#endif