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cmdline.h
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cmdline.h
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#ifndef __COMMANDLINE
#define __COMMANDLINE
#include <vector>
#include <string>
enum class CompressType { gzip, bzip2, uncompressed };
CompressType operator<<(CompressType& val, const std::string& str);
#include "bindopt.h"
struct ParametersCommon {
std::string seq_filename;
std::string output_filename;
std::string log_filename;
CompressType zip;
unsigned int kmer_length;
unsigned int threads;
unsigned long ram_limit;
bool verbose;
bool help;
ParametersCommon();
explicit ParametersCommon(bindopt::Options &options);
void get_options(bindopt::Options &options);
};
struct ParametersBuild : ParametersCommon {
std::string mask;
ParametersBuild();
explicit ParametersBuild(bindopt::Options &options);
void get_options(bindopt::Options &options);
};
struct ParametersFilter : ParametersCommon {
std::string seq_mate_filename;
std::string index_filename;
unsigned int min_kmer_threshhold;
ParametersFilter();
explicit ParametersFilter(bindopt::Options &options);
void get_options(bindopt::Options &options);
};
void print_help( void);
#endif