#include "command.hpp"
#include "sequence.hpp"
+#include "counttable.h"
/************************************************************/
struct seqRNode {
void help() { m->mothurOut(getHelpString()); }
private:
+ CountTable ct;
bool abort;
- string fastafile, namefile, outputDir;
+ string fastafile, namefile, countfile, outputDir;
int diffs, percent;
vector<seqRNode> alignSeqs;
map<string, string> names; //represents the names file first column maps to second column