string getCommandName() { return "consensus.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+ string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
map<string, string> fastaMap;
map<string, string> nameMap;
map<string, string> nameFileMap;
+ int cutoff;
int readFasta();
int readNames();
int processList(ListVector*&);
string getConsSeq(string, ofstream&, string&, int);
- char getBase(vector<int>);
+ char getBase(vector<int>, int);
};
#endif