public:
SeqErrorCommand(string);
SeqErrorCommand();
- ~SeqErrorCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~SeqErrorCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "seq.error"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
map<string,int> getWeights();
Compare getErrors(Sequence, Sequence);
void printErrorHeader();
- void printErrorData(Compare);
-
- string queryFileName, referenceFileName, namesFileName, errorSummaryFileName, errorSeqFileName, outputDir;
+ void printErrorData(Compare, int);
+ 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> >);
+
+ string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
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;
};
#endif