#include "command.hpp"
#include "fastamap.h"
-#include "globaldata.hpp"
/* 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. */
class DeconvoluteCommand : public Command {
public:
- DeconvoluteCommand(string);
- ~DeconvoluteCommand() { delete fastamap; };
+ DeconvoluteCommand(string);
+ ~DeconvoluteCommand() { };
int execute();
void help();
private:
- GlobalData* globaldata;
- FastaMap* fastamap;
- ifstream in;
- ofstream out, outFasta;
- string filename, outputFileName, outFastafile;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort;
-
+ string inFastaName, oldNameMapFName, outputDir;
+ bool abort;
};
#endif