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cmd_query_bf.h
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cmd_query_bf.h
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#ifndef cmd_query_bf_H
#define cmd_query_bf_H
#include <string>
#include <cstdlib>
#include <cstdint>
#include <iostream>
#include "bloom_filter.h"
#include "commands.h"
class QueryBFCommand: public Command
{
public:
QueryBFCommand(const std::string& name): Command(name) {}
virtual ~QueryBFCommand();
virtual void short_description (std::ostream& s);
virtual void usage (std::ostream& s, const std::string& message="");
virtual void debug_help (std::ostream& s);
virtual void parse (int _argc, char** _argv);
virtual int execute (void);
virtual void read_queries (void);
std::vector<std::string> bfFilenames;
std::vector<std::string> queryFilenames;
std::vector<double> queryThresholds;
double generalQueryThreshold;
bool distinctKmers;
bool reportAllKmers;
std::vector<Query*> queries;
};
#endif // cmd_query_bf_H