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0.16.0 release

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chhylp123
2021-08-22 21:58:00 -04:00
parent 37b07e4d33
commit e230b3a55f
10 changed files with 126 additions and 85 deletions
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htab.cpp
+10 -72
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@@ -130,6 +130,7 @@ typedef struct {
typedef struct {
int k, pre, n_hash, n_shift;
uint64_t tot; ///number of distinct k-mers
uint64_t bs;
ha_ct1_t *h;
} ha_ct_t;
@@ -851,7 +852,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
if (p->pt && !(p->flag&HAF_COUNT_REFINE)) free(s->buf[i].b);
else free(s->buf[i].a);
}
if (p->ct) p->ct->tot += n_ins;
if (p->ct) p->ct->tot += n_ins, p->ct->bs += s->sum_len;
if (p->pt) p->pt->tot_pos += n_ins;
free(s->buf);
#if 0
@@ -945,6 +946,7 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
///building a large hash table consisting of 4096 small hash tables
pl.ct = ha_ct_init(opt->k, opt->pre, opt->bf_n_hash, opt->bf_shift);
}
if(pl.ct) pl.ct->bs = 0;
kt_pipeline(3, worker_count, &pl, 3);
if (read_rs) {
destory_UC_Read(&pl.ucr);
@@ -961,6 +963,7 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
{
int i;
int64_t n_seq = 0;
uint64_t n_bs = 0;
yak_copt_t opt;
ha_ct_t *h = 0;
assert(!(flag & HAF_RS_WRITE_LEN) || !(flag & HAF_RS_WRITE_SEQ)); // not both
@@ -984,8 +987,11 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
opt.adaLen = (keep_adapter? asm_opt->adapterLen : 0);
opt.min_rcnt = (low_freq?*low_freq:-1);
///asm_opt->num_reads is the number of fastq files
for (i = 0; i < asm_opt->num_reads; ++i)
for (i = n_bs = 0; i < asm_opt->num_reads; ++i){
h = yak_count(&opt, asm_opt->read_file_names[i], flag|HAF_CREATE_NEW, p0, h, flt_tab, rs, us, &n_seq);
if(h) n_bs += h->bs;
}
if(h) h->bs = n_bs;
if (h && opt.bf_shift > 0)
ha_ct_destroy_bf(h);
return h;
@@ -1140,7 +1146,7 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int i
if(!(ex_flag & HAF_SKIP_READ))
{
ha_ct_hist(h, cnt, asm_opt->thread_num);
peak_hom = ha_analyze_count(YAK_N_COUNTS, asm_opt->min_hist_kmer_cnt, cnt, &peak_het);
peak_hom = ha_analyze_count(YAK_N_COUNTS, asm_opt->min_hist_kmer_cnt, asm_opt->hg_size>0?(h->bs/asm_opt->hg_size):(-1), 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);
///in default, asm_opt->high_factor = 5.0
@@ -1155,38 +1161,6 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int i
return (void*)flt_tab;
}
void *ha_ft_gen_worse(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int is_hp_mode)
{
yak_ft_t *flt_tab;
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het, cutoff = YAK_MAX_COUNT - 1, ex_flag = 0;
if(is_hp_mode) ex_flag = HAF_RS_READ|HAF_SKIP_READ;
ha_ct_t *h;
h = ha_count(asm_opt, HAF_COUNT_ALL|HAF_RS_WRITE_LEN|ex_flag, NULL, NULL, rs, NULL, 1, NULL);
if((asm_opt->flag & HA_F_VERBOSE_GFA))
{
write_ct_index((void*)h, asm_opt->output_file_name);
// load_ct_index(&ha_ct_table, asm_opt->output_file_name);
// debug_ct_index((void*)h, ha_ct_table);
// debug_ct_index(ha_ct_table, (void*)h);
// ha_ct_destroy((ha_ct_t *)ha_ct_table);
}
if(!(ex_flag & HAF_SKIP_READ))
{
ha_ct_hist(h, cnt, asm_opt->thread_num);
peak_hom = ha_analyze_count(YAK_N_COUNTS, asm_opt->min_hist_kmer_cnt, 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);
}
ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
flt_tab = gen_hh(h, 1/**asm_opt->max_kmer_cnt**/);
ha_ct_destroy(h);
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;
}
ha_pt_t *ha_pt_gen_dp(const hifiasm_opt_t *asm_opt, ha_ct_t *ct, int flag, int n_thread, const void *flt_tab, All_reads *rs, int peak_hom, int peak_het)
{
int low_freq = mz_low_b(peak_hom, peak_het);
@@ -1203,42 +1177,6 @@ ha_pt_t *ha_pt_gen_dp(const hifiasm_opt_t *asm_opt, ha_ct_t *ct, int flag, int n
return pt;
}
ha_pt_t *ha_pt_gen_worst(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)
{
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het, extra_flag1, extra_flag2;
ha_ct_t *ct;
ha_pt_t *pt;
if (read_from_store) {///if reads have already been read
extra_flag1 = extra_flag2 = HAF_RS_READ;
} else if (rs->total_reads == 0) {///if reads & length have not been scanned
extra_flag1 = HAF_RS_WRITE_LEN;
extra_flag2 = HAF_RS_WRITE_SEQ;
} else {///if length has been loaded but reads have not
extra_flag1 = HAF_RS_WRITE_SEQ;
extra_flag2 = HAF_RS_READ;
}
if(is_hp_mode) extra_flag1 |= HAF_SKIP_READ, extra_flag2 |= HAF_SKIP_READ;
ct = ha_count(asm_opt, HAF_COUNT_EXACT|extra_flag1, NULL, flt_tab, rs, NULL, 1, NULL);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
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, asm_opt->min_hist_kmer_cnt, cnt, &peak_het);
if (hom_cov) *hom_cov = peak_hom;
if (het_cov) *het_cov = peak_het;
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
///here ha_ct_shrink is mostly used to remove k-mer appearing only 1 time
ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
pt = ha_pt_gen_dp(asm_opt, ct, HAF_COUNT_EXACT|extra_flag2, asm_opt->thread_num, flt_tab, rs, peak_hom, peak_het);
//ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,
yak_realtime(), yak_cpu_usage(), (long)pt->tot_pos);
return pt;
}
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)
{
int64_t cnt[YAK_N_COUNTS], tot_cnt;
@@ -1261,7 +1199,7 @@ ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_f
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, asm_opt->min_hist_kmer_cnt, cnt, &peak_het);
peak_hom = ha_analyze_count(YAK_N_COUNTS, asm_opt->min_hist_kmer_cnt, asm_opt->hg_size>0?(ct->bs/asm_opt->hg_size):(-1), cnt, &peak_het);
if (hom_cov) *hom_cov = peak_hom;
if (het_cov) *het_cov = peak_het;
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);