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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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CommandLines.h
+28 -16
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@@ -3,25 +3,37 @@
#include <pthread.h>
#define VERBOSE 0
extern char* read_file_name;
extern char* output_file_name;
extern int thread_num;
extern int k_mer_length;
extern int k_mer_min_freq;
extern int k_mer_max_freq;
extern int load_index_from_disk;
extern int write_index_to_disk;
extern int number_of_round;
extern int roundID;
extern int coverage;
extern int read_graph;
extern int c_round;
extern char* required_read_name;
extern int adapterLen;
typedef struct {
char* read_file_name;
char* output_file_name;
char* required_read_name;
int thread_num;
int k_mer_length;
int k_mer_min_freq;
int k_mer_max_freq;
int load_index_from_disk;
int write_index_to_disk;
int number_of_round;
int adapterLen;
int clean_round;
int complete_threads;
int roundID;
float min_drop_rate;
float max_drop_rate;
long long pop_bubble_size;
long long num_bases;
long long num_corrected_bases;
long long num_recorrected_bases;
} hifiasm_opt_t;
int CommandLine_process (int argc, char *argv[]);
extern hifiasm_opt_t asm_opt;
void init_opt(hifiasm_opt_t* asm_opt);
void clear_opt(hifiasm_opt_t* asm_opt, int last_round);
int CommandLine_process (int argc, char *argv[], hifiasm_opt_t* asm_opt);
double Get_T(void);
#endif