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phasing speedup

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chhylp123
2026-04-11 22:33:18 -04:00
parent 815d709fb9
commit ba8627fb23
13 changed files with 1055 additions and 186 deletions
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htab.cpp
+17 -19
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@@ -1120,13 +1120,26 @@ void debug_ct_index(void* q_ct_idx, void* r_ct_idx)
/*************************
* High-level interfaces *
*************************/
void *ha_ft_ul_gen(const hifiasm_opt_t *asm_opt, ma_utg_v *us, int k, int w, int cutoff)
int64_t ha_ct_ug_cutoff(ha_ct_t *h, int64_t num_thre, double cut_rate)
{
yak_ft_t *flt_tab;
ha_ct_t *h;
int64_t cnt[YAK_N_COUNTS], k, tot_n = 0, tot_cutn = 0;
ha_ct_hist(h, cnt, num_thre);
for (k = tot_n = 0; k < YAK_N_COUNTS; k++) tot_n += cnt[k];
tot_cutn = tot_n - (tot_n*cut_rate);
for (k = tot_n = 0; k < YAK_N_COUNTS && tot_n < tot_cutn; k++) tot_n += cnt[k];
return k;
}
void *ha_ft_ul_gen(const hifiasm_opt_t *asm_opt, ma_utg_v *us, int k, int w, int cutoff, int max_cutoff)
{
yak_ft_t *flt_tab; ha_ct_t *h;
///HAF_COUNT_EXACT ---> no bf; HAF_COUNT_ALL ---> no minimizer
h = ha_count(asm_opt, HAF_COUNT_ALL|HAF_UG_READ, !(asm_opt->flag&HA_F_NO_HPC), k, w, NULL, NULL, NULL, us, 0, NULL, 0);
if(cutoff < 0) cutoff = ha_ct_ug_cutoff(h, asm_opt->thread_num, 0.0002);
if(cutoff > max_cutoff) cutoff = max_cutoff;
// cutoff = (int)(asm_opt->hom_cov * asm_opt->high_factor);
if (cutoff > YAK_MAX_COUNT - 1) cutoff = YAK_MAX_COUNT - 1;
// fprintf(stderr, "[M::%s::] cutoff->%d\n\n", __func__, cutoff);
@@ -1138,21 +1151,6 @@ void *ha_ft_ul_gen(const hifiasm_opt_t *asm_opt, ma_utg_v *us, int k, int w, int
return (void*)flt_tab;
}
// int64_t ha_ct_ug_cutoff(ha_ct_t *h, int64_t num_thre, double cut_rate, double cut_an_rate)
// {
// int64_t cnt[YAK_N_COUNTS], k, tot_n = 0, tot_cutn = 0, tot_an = 0, tot_cut_an = 0, tot_k = 0, tot_ak = 0;
// ha_ct_hist(h, cnt, num_thre);
// for (k = tot_n = tot_an = 0; k < YAK_N_COUNTS; k++) {
// tot_n += cnt[k]; tot_an += cnt[k]*k;
// }
// tot_cutn = tot_n - (tot_n*cut_rate);
// tot_cut_an = tot_an - (tot_an*cut_an_rate);
// }
void *ha_ft_ug_gen(hifiasm_opt_t *asm_opt, ma_utg_v *us, int is_HPC, int k, int w, int min_freq, int max_freq)
{
yak_ft_t *flt_tab;