xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-28 10:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

option to skip k-mer filtering

Browse Source
This commit is contained in:
Heng Li
2020-03-27 22:32:39 -04:00
parent 19648873b9
commit 5e16483b43
4 changed files with 29 additions and 9 deletions
Download Patch File Download Diff File Expand all files Collapse all files
htab.cpp
+22 -6
View File
@@ -764,7 +764,7 @@ int ha_ft_isflt(const void *hh, uint64_t y)
void ha_ft_destroy(void *h)
{
yak_ft_destroy((yak_ft_t*)h);
if (h) yak_ft_destroy((yak_ft_t*)h);
}
/*************************
@@ -794,20 +794,36 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, 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)
{
int64_t cnt[YAK_N_COUNTS], tot_cnt;
int peak_hom, peak_het, i, extra_flag = read_from_store? HAF_RS_READ : HAF_RS_WRITE_SEQ;
int peak_hom, peak_het, i, extra_flag1, extra_flag2;
ha_ct_t *ct;
ha_pt_t *pt;
ct = ha_count(asm_opt, HAF_COUNT_EXACT|extra_flag, NULL, flt_tab, rs);
if (read_from_store) {
extra_flag1 = extra_flag2 = HAF_RS_READ;
} else if (rs->total_reads == 0) {
extra_flag1 = HAF_RS_WRITE_LEN;
extra_flag2 = HAF_RS_WRITE_SEQ;
} else {
extra_flag1 = HAF_RS_WRITE_SEQ;
extra_flag2 = HAF_RS_READ;
}
ct = ha_count(asm_opt, HAF_COUNT_EXACT|extra_flag1, NULL, flt_tab, rs);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)ct->tot);
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 (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
for (i = 2, tot_cnt = 0; i <= YAK_MAX_COUNT - 1; ++i) tot_cnt += cnt[i] * i;
if (flt_tab == 0) {
int cutoff = (int)(peak_hom * asm_opt->high_factor);
if (cutoff > YAK_MAX_COUNT - 1) cutoff = YAK_MAX_COUNT - 1;
ha_ct_shrink(ct, 2, cutoff, asm_opt->thread_num);
for (i = 2, tot_cnt = 0; i <= cutoff; ++i) tot_cnt += cnt[i] * i;
} else {
ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
for (i = 2, tot_cnt = 0; i <= YAK_MAX_COUNT - 1; ++i) tot_cnt += cnt[i] * i;
}
pt = ha_pt_gen(ct, asm_opt->thread_num);
ha_count(asm_opt, HAF_COUNT_EXACT|HAF_RS_READ, pt, flt_tab, rs);
ha_count(asm_opt, HAF_COUNT_EXACT|extra_flag2, pt, flt_tab, rs);
assert((uint64_t)tot_cnt == pt->tot_pos);
//ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,