xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-25 22:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r192: estimate buffer memory

Browse Source
This commit is contained in:
Heng Li
2020-04-05 11:17:12 -04:00
parent 8c27dbb52f
commit f0c53e9948
9 changed files with 77 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files
htab.cpp
+5 -5
View File
@@ -657,7 +657,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
free(s->buf);
#if 0
fprintf(stderr, "[M::%s::%.3f*%.2f] processed %ld sequences; %ld %s in the hash table\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)s->n_seq0 + s->n_seq,
yak_realtime(), yak_cpu_usage(), (long)s->n_seq0 + s->n_seq,
(long)(p->pt? p->pt->tot_pos : p->ct->tot), p->pt? "positions" : "distinct k-mers");
#endif
free(s);
@@ -786,8 +786,8 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs)
ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
flt_tab = gen_hh(h);
ha_ct_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> filtered out %ld k-mers occurring %d or more times\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)kh_size(flt_tab), cutoff);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> filtered out %ld k-mers occurring %d or more times\n", __func__,
yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb(), (long)kh_size(flt_tab), cutoff);
return (void*)flt_tab;
}
@@ -808,7 +808,7 @@ ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_f
}
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);
yak_realtime(), yak_cpu_usage(), (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);
@@ -827,6 +827,6 @@ ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_f
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__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)pt->tot_pos);
yak_realtime(), yak_cpu_usage(), (long)pt->tot_pos);
return pt;
}