#include "command.hpp"
#include "sequence.hpp"
+#include "counttable.h"
/************************************************************/
struct seqRNode {
vector<string> setParameters();
string getCommandName() { return "cluster.fragments"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
+ string getDescription() { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
int execute();
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