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config.hpp
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config.hpp
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#ifndef __CONFIG_HPP__
#define __CONFIG_HPP__
#include <string>
#include <vector>
class Config {
public:
Config(int argc, const char *argv[]);
bool verbose = false;
bool reverse = false;
bool fasta_anno = false;
bool wavelet_trie = false;
unsigned int k = 3;
unsigned int distance = 0;
unsigned int alignment_length = 0;
unsigned int bloom_num_hash_functions = 0;
unsigned int bloom_test_num_kmers = 0;
unsigned int p = 1;
unsigned int num_permutations = 0;
double bloom_fpp = -1;
double bloom_bits_per_edge = -1;
double discovery_fraction = 1.0;
std::vector<std::string> fname;
std::string outfbase;
std::string infbase;
std::string dbpath;
std::string refpath;
std::string fasta_header_delimiter;
enum IdentityType {
NO_IDENTITY = -1,
BUILD,
UPDATE,
MAP,
PERMUTATION,
QUERY,
STATS,
COMPRESS
};
IdentityType identity = NO_IDENTITY;
void print_usage(const std::string &prog_name,
IdentityType identity = NO_IDENTITY);
};
#endif // __CONFIG_HPP__