public:
TrimSeqsCommand(string);
TrimSeqsCommand();
- ~TrimSeqsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~TrimSeqsCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "trim.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
- void getOligos(vector<string>&, vector<string>&);
+ void getOligos(vector<vector<string> >&, vector<vector<string> >&);
int stripBarcode(Sequence&, QualityScores&, int&);
int stripForward(Sequence&, QualityScores&, int&);
bool stripReverse(Sequence&, QualityScores&);
bool cullAmbigs(Sequence&);
bool compareDNASeq(string, string);
int countDiffs(string, string);
- map<string, vector<string> > outputTypes;
bool abort;
string fastaFile, oligoFile, qFileName, groupfile, outputDir;
map<string, int> primers;
map<string, int> combos;
map<string, int> groupToIndex;
-
+ vector<string> primerNameVector; //needed here?
+ vector<string> barcodeNameVector; //needed here?
+ map<string, int> groupCounts;
+
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<linePair*> qLines;
- int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
- int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
+ int driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);
+ int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
};