public:
GetSeqsCommand(string);
+ GetSeqsCommand();
~GetSeqsCommand(){};
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
set<string> names;
vector<string> outputNames;
- string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
- bool abort;
+ string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ bool abort, dups;
+ map<string, vector<string> > outputTypes;
int readFasta();
int readName();
int readAccnos();
int readList();
int readTax();
+ int readQual();
+ int compareAccnos();
};