string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
-
+ string getDescription() { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
- void getOligos(vector<vector<string> >&, vector<vector<string> >&);
+ bool 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 compareDNASeq(string, string);
int countDiffs(string, string);
- bool abort;
- string fastaFile, oligoFile, qFileName, groupfile, outputDir;
+ bool abort, createGroup;
+ string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
bool flip, allFiles, qtrim;
int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
vector<string> primerNameVector; //needed here?
vector<string> barcodeNameVector; //needed here?
map<string, int> groupCounts;
+ map<string, string> nameMap;
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<linePair*> qLines;
- 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 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>&);
};