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bll.h
64 lines (54 loc) · 1.56 KB
/
bll.h
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#include "common.h"
#include "extract.h"
//#include "cycle.h"
#include "cluster.h"
#include "intersperse.h"
//class All:public Extract,public Cycle{
class All{
public:
All();
void all_exe(int argc, char**argv);
string o,o1,kmer_for_cycle_find,kmer_for_copy_estimate,kmer_for_path_find; //output
vector<string> files,files1,files2; //files
double c1; //copy difference
string c1_string;
uint64_t c2; //copy difference
uint64_t t; //num_threads
bool d; //data type
int repeat_type;
//mode
bool bool_single, bool_compare;
//jellyfish_file
bool jf_file_exist, jf_file1_exist, jf_file2_exist;
bool dump_file_exist, dump_file1_exist, dump_file2_exist;
bool histo_file_exist, histo_file1_exist, histo_file2_exist;
//stopwatch
bool bool_stopwatch;
//tandem
bool tandem_exist;
int max_l; //max_length
int max_n; //max_nodes
int max_d; //max_depth
//cluster
int mismatch;
//intersperse
int max_L; //max_length
int max_N; //max_nodes
int max_D; //max_depth
//peak
uint64_t p;
uint64_t p1;
uint64_t p2;
double read_coverage;
string jf_file, jf_file1, jf_file2;
string dump_file, dump_file1, dump_file2;
string histo_file, histo_file1, histo_file2;
void print_all_usage(void);
void option_all_init(void);
int option_all_parse(int argc, char**argv);
void opt_all_to_extract(Extract *extract);
void peak_to_opt_all(uint64_t *peak, uint64_t *peak1, uint64_t *peak2);
void opt_all_to_cycle(Cycle *cycle);
void opt_all_to_cluster(Cluster *cluster);
void opt_all_to_intersperse(Intersperse *intersperse);
};