public:
ChimeraPintailCommand(string);
- ~ChimeraPintailCommand();
- int execute();
- void help();
+ ChimeraPintailCommand();
+ ~ChimeraPintailCommand(){}
+ vector<string> setParameters();
+ string getCommandName() { return "chimera.pintail"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
Chimera* chimera;
vector<string> outputNames;
vector<string> fastaFileNames;
-
-
};
/***********************************************************/