xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-29 03:28:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r201: automatically adjust -N

Browse Source
This commit is contained in:
Heng Li
2020-04-05 22:43:01 -04:00
parent 3773610532
commit adbc65feda
5 changed files with 43 additions and 33 deletions
Download Patch File Download Diff File Expand all files Collapse all files
htab.cpp
+4 -2
View File
@@ -771,7 +771,7 @@ void ha_ft_destroy(void *h)
* High-level interfaces *
*************************/
void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs)
void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov)
{
yak_ft_t *flt_tab;
int64_t cnt[YAK_N_COUNTS];
@@ -780,6 +780,7 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs)
h = ha_count(asm_opt, HAF_COUNT_ALL|HAF_RS_WRITE_LEN, NULL, NULL, rs);
ha_ct_hist(h, cnt, asm_opt->thread_num);
peak_hom = ha_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
if (hom_cov) *hom_cov = peak_hom;
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
cutoff = (int)(peak_hom * asm_opt->high_factor);
if (cutoff > YAK_MAX_COUNT - 1) cutoff = YAK_MAX_COUNT - 1;
@@ -791,7 +792,7 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs)
return (void*)flt_tab;
}
ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, All_reads *rs)
ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, All_reads *rs, int *hom_cov)
{
int64_t cnt[YAK_N_COUNTS], tot_cnt;
int peak_hom, peak_het, i, extra_flag1, extra_flag2;
@@ -812,6 +813,7 @@ ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_f
ha_ct_hist(ct, cnt, asm_opt->thread_num);
fprintf(stderr, "[M::%s] count[%d] = %ld (for sanity check)\n", __func__, YAK_MAX_COUNT, (long)cnt[YAK_MAX_COUNT]);
peak_hom = ha_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
if (hom_cov) *hom_cov = peak_hom;
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
if (flt_tab == 0) {
int cutoff = (int)(peak_hom * asm_opt->high_factor);