GroupMap* groupMap;
struct linePair {
- unsigned long int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
- void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
- int stripBarcode(Sequence&, QualityScores&, int&);
- int stripForward(Sequence&, QualityScores&, int&);
- bool stripReverse(Sequence&, QualityScores&);
-
+ bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
bool keepFirstTrim(Sequence&, QualityScores&);
bool removeLastTrim(Sequence&, QualityScores&);
-
bool cullLength(Sequence&);
bool cullHomoP(Sequence&);
bool cullAmbigs(Sequence&);
- bool compareDNASeq(string, string);
- int countDiffs(string, string);
- bool abort;
+ bool abort, createGroup;
string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
bool flip, allFiles, qtrim;
int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);
int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
- int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
+ int setLines(string, string, vector<unsigned long long>&, vector<unsigned long long>&);
};
#endif