#include "nameassignment.hpp"
#include "cluster.hpp"
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "nameassignment.hpp"
#include "cluster.hpp"
#include "hcluster.h"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
string getDescription() { return "cluster your sequences into OTUs using a blast file"; }
string getHelpString();
string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
string getDescription() { return "cluster your sequences into OTUs using a blast file"; }
- string blastfile, method, namefile, overlapFile, distFile, outputDir;
+ string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);