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;
mismatches = 0;
total = 0;
errorRate = 1.0000;
+ sequence = "";
}
};
void printErrorHeader();
void printErrorData(Compare);
- string queryFileName, referenceFileName, namesFileName, errorFileName, outputDir;
+ string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
double threshold;
int numRefs;
- ofstream errorFile;
+ ofstream errorSummaryFile, errorSeqFile;
vector<string> outputNames;
map<string, vector<string> > outputTypes;