#include "command.hpp"
#include "readblast.h"
-#include "sparsematrix.hpp"
#include "nameassignment.hpp"
#include "cluster.hpp"
#include "hcluster.h"
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
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"; }
double cutoff;
float penalty;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, merge, hard, large;
+ bool abort, minWanted, hclusterWanted, merge, hard;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);
void sortHclusterFiles(string, string);
vector<seqDist> getSeqs(ifstream&);
- void createRabund(CountTable*, ListVector*);
+ void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};