private:
bool abort;
+
+ struct linePair {
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ };
+
+ vector<int> processIDS; //processid
+ vector<linePair> lines;
+ vector<linePair> qLines;
+ vector<linePair> rLines;
void getReferences();
map<string,int> getWeights();
Compare getErrors(Sequence, Sequence);
- void printErrorHeader();
- void printErrorData(Compare, int);
+ void printErrorHeader(ofstream&);
+ void printErrorData(Compare, int, ofstream&, ofstream&);
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> >);
+
+ int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+ int driver(string, string, string, string, string, string, linePair, linePair, linePair);
+ int createProcesses(string, string, string, string, string, string);
string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
double threshold;
- bool ignoreChimeras;
+ bool ignoreChimeras, filter;
int numRefs, processors;
- int maxLength;
- ofstream errorSummaryFile, errorSeqFile;
+ int maxLength, totalBases, totalMatches;
+ //ofstream errorSummaryFile, errorSeqFile;
vector<string> outputNames;
vector<Sequence> referenceSeqs;
vector<vector<int> > substitutionMatrix;
+ vector<vector<int> > qualForwardMap;
+ vector<vector<int> > qualReverseMap;
+ vector<int> misMatchCounts;
+ map<char, vector<int> > qScoreErrorMap;
+ map<char, vector<int> > errorForward;
+ map<char, vector<int> > errorReverse;
+ map<string, int> weights;
+ vector<string> megaAlignVector;
+
};
#endif