#include "command.hpp"
#include "fastamap.h"
+#include "counttable.h"
/* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
containing 2 columns. The first being the groupname and the second the list of identical sequence names. */
vector<string> setParameters();
string getCommandName() { return "unique.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
private:
- string inFastaName, oldNameMapFName, outputDir;
+ string inFastaName, oldNameMapFName, outputDir, countfile;
vector<string> outputNames;
bool abort;