#include "command.hpp"
#include "listvector.hpp"
+#include "counttable.h"
class ConsensusSeqsCommand : public Command {
public:
vector<string> setParameters();
string getCommandName() { return "consensus.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
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"; }
private:
+ CountTable ct;
bool abort, allLines;
- string fastafile, listfile, namefile, label, outputDir;
+ string fastafile, listfile, namefile, countfile, label, outputDir;
set<string> labels;
vector<string> outputNames;
map<string, string> fastaMap;
map<string, string> nameMap;
- map<string, string> nameFileMap;
- int cutoff;
+ map<string, int> nameFileMap;
+ int cutoff, seqLength;
int readFasta();
int readNames();
int processList(ListVector*&);
- string getConsSeq(string, ofstream&, string&, int);
+ string getConsSeq(string, ofstream&, int);
char getBase(vector<int>, int);
};