#include "rabundvector.hpp"
#include "inputdata.h"
#include "sequence.hpp"
+#include "counttable.h"
class SubSampleCommand : public Command {
private:
bool abort, pickedGroups, allLines, persample;
- string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+ string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
set<string> labels; //holds labels to be used
string groups, label, outputDir;
vector<string> Groups, outputNames;
int size;
vector<string> names;
map<string, vector<string> > nameMap;
+ CountTable ct;
int getSubSampleShared();
int getSubSampleList();