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Merge branch 'chain-tune' into merge2

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This commit is contained in:
Heng Li
2020-04-05 12:07:13 -04:00
parent ac3fcc339a f0c53e9948
commit 5917aa2f36
28 changed files with 2068 additions and 4528 deletions
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CommandLines.h
+12 -4
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@@ -3,6 +3,8 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r192"
#define VERBOSE 0
#define VERBOSE_GFA 1
@@ -15,6 +17,12 @@ typedef struct {
char* mat_index;
int thread_num;
int k_mer_length;
int mz_win;
int bf_shift;
float high_factor;
int no_HPC;
int no_kmer_flt;
int max_n_chain;
int k_mer_min_freq;
int k_mer_max_freq;
int load_index_from_disk;
@@ -22,7 +30,6 @@ typedef struct {
int number_of_round;
int adapterLen;
int clean_round;
int complete_threads;
int roundID;
int max_hang_Len;
int gap_fuzz;
@@ -41,6 +48,7 @@ typedef struct {
long long num_bases;
long long num_corrected_bases;
long long num_recorrected_bases;
long long mem_buf;
long long coverage;
} hifiasm_opt_t;
@@ -48,8 +56,8 @@ extern hifiasm_opt_t asm_opt;
void init_opt(hifiasm_opt_t* asm_opt);
void destory_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);
void clear_opt(hifiasm_opt_t* asm_opt, int round);
int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt);
double Get_T(void);
#endif
#endif