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chhylp123
2021-08-12 11:16:10 -04:00
parent 6ea66e1290
commit bfff640a82
8 changed files with 646 additions and 113 deletions
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htab.h
+16 -1
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@@ -5,6 +5,11 @@
#include "Process_Read.h"
#include "CommandLines.h"
typedef struct {
int n, m;
uint64_t *a;
} st_mt_t;
typedef struct {
uint64_t x; ///x is the hash key
///rid is the read id, pos is the end pos of this minimizer, rev is the direction
@@ -75,6 +80,7 @@ ha_pt_t *ha_pt_ug_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, ma_utg_
ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, int is_hp_mode, All_reads *rs, int *hom_cov, int *het_cov);
void ha_pt_destroy(ha_pt_t *h);
const ha_idxpos_t *ha_pt_get(const ha_pt_t *h, uint64_t hash, int *n);
const int ha_pt_cnt(const ha_pt_t *h, uint64_t hash);
int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name);
int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name);
@@ -95,11 +101,20 @@ double yak_cpu_usage(void);
void ha_triobin(const hifiasm_opt_t *opt);
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct);
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, ha_pt_t *pt, int min_freq, int32_t dp_min_len, float dp_e, st_mt_t *mt);
int ha_analyze_count(int n_cnt, int start_cnt, const int64_t *cnt, int *peak_het);
void print_hist_lines(int n_cnt, int start_cnt, const int64_t *cnt);
void debug_adapter(const hifiasm_opt_t *asm_opt, All_reads *rs);
inline int mz_low_b(int peak_hom, int peak_het)
{
int low_freq = 2;
if(peak_het > 0) low_freq = peak_het/2;
else if(peak_hom > 0) low_freq = peak_hom/4;
if(low_freq < 2) low_freq = 2;
return low_freq;
}
static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function
{
key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;