#include "command.hpp"
#include "listvector.hpp"
+#include "counttable.h"
class ConsensusSeqsCommand : public Command {
public:
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);
};