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