*/
#include "command.hpp"
-#include "utilities.hpp"
#include "fastamap.h"
-#include "globaldata.hpp"
-/* The deconvolute command reads a fasta file, finds the duplicate sequences and outputs a names file
+/* 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. */
-using namespace std;
class DeconvoluteCommand : public Command {
public:
- DeconvoluteCommand() {};
- ~DeconvoluteCommand() { delete fastamap; };
- int execute();
+ DeconvoluteCommand(string);
+ DeconvoluteCommand();
+ ~DeconvoluteCommand() {}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
private:
- GlobalData* globaldata;
- FastaMap* fastamap;
- ifstream in;
- ofstream out, outFasta;
- string filename, outputFileName, outFastafile;
+ string inFastaName, oldNameMapFName, outputDir;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+ bool abort;
};
#endif