#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. */
DeconvoluteCommand(string);
DeconvoluteCommand();
~DeconvoluteCommand() {}
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+
+ vector<string> setParameters();
+ string getCommandName() { return "unique.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+
+ 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"; }
+
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
- string inFastaName, oldNameMapFName, outputDir;
+ string inFastaName, oldNameMapFName, outputDir, countfile;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
bool abort;
};