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a bit refactoring for the next change

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This commit is contained in:
Heng Li
2020-10-29 18:24:47 -04:00
parent ef8c047559
commit f37c4e29fa
6 changed files with 26 additions and 29 deletions
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29
htab.cpp
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@@ -1,4 +1,3 @@
#include <stdint.h>
#include <zlib.h>
#include <stdio.h>
#include <string.h>
@@ -557,7 +556,7 @@ static void worker_for_mz(void *data, long i, int tid)
ha_mz1_v *b = &s->mz_buf[tid];
s->mz_buf[tid].n = 0;
///s->p->opt->w = 51, s->p->opt->k
ha_sketch_query(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->n_seq0 + i, s->p->opt->is_HPC, b, s->p->flt_tab, 0, 0);
ha_sketch(s->seq[i], s->len[i], s->p->opt->w, s->p->opt->k, s->n_seq0 + i, s->p->opt->is_HPC, b, s->p->flt_tab, 0, 0);
s->mz[i].n = s->mz[i].m = b->n;
MALLOC(s->mz[i].a, b->n);
memcpy(s->mz[i].a, b->a, b->n * sizeof(ha_mz1_t));
@@ -803,12 +802,15 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const voi
* High count filter table *
***************************/
// Warning: the max count is 32767
KHASHL_MAP_INIT(static klib_unused, yak_ft_t, yak_ft, uint64_t, int16_t, kh_hash_dummy, kh_eq_generic)
static yak_ft_t *gen_hh(const ha_ct_t *h)
static yak_ft_t *gen_hh(const ha_ct_t *h, int max_cnt)
{
int i;
yak_ft_t *hh;
if (max_cnt > YAK_MAX_COUNT - 1) max_cnt = YAK_MAX_COUNT - 1;
if (max_cnt > INT16_MAX - 1) max_cnt = INT16_MAX - 1;
hh = yak_ft_init();
yak_ft_resize(hh, h->tot * 2);
for (i = 0; i < 1<<h->pre; ++i) {
@@ -819,28 +821,22 @@ static yak_ft_t *gen_hh(const ha_ct_t *h)
uint64_t y = kh_key(ht, k) >> h->pre << YAK_COUNTER_BITS | i;
int absent;
l = yak_ft_put(hh, y, &absent);
if (absent)
kh_val(hh, l) = kh_key(ht, k)&YAK_MAX_COUNT;
if (absent) {
int cnt = kh_key(ht, k) & YAK_MAX_COUNT;
kh_val(hh, l) = cnt > max_cnt? INT16_MAX : cnt;
}
}
}
}
return hh;
}
int ha_ft_isflt(const void *hh, uint64_t y)
int32_t ha_ft_cnt(const void *hh, uint64_t y)
{
yak_ft_t *h = (yak_ft_t*)hh;
khint_t k;
k = yak_ft_get(h, y);
return k == kh_end(h)? 0 : 1;
}
int ha_ft_cnt(const void *hh, uint64_t y)
{
yak_ft_t *h = (yak_ft_t*)hh;
khint_t k;
k = yak_ft_get(h, y);
return k == kh_end(h)? 0 : kh_val(h, k);
return k == kh_end(h)? 0 : kh_val(h, k) == INT16_MAX? INT32_MAX : kh_val(h, k);
}
void ha_ft_destroy(void *h)
@@ -906,7 +902,7 @@ void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int i
if (cutoff > YAK_MAX_COUNT - 1) cutoff = YAK_MAX_COUNT - 1;
}
ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
flt_tab = gen_hh(h);
flt_tab = gen_hh(h, 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);
@@ -970,7 +966,6 @@ int query_ct_index(void* ct_idx, uint64_t hash)
return kh_key(g->h, k)&YAK_MAX_COUNT;
}
int write_ct_index(void *i_ct_idx, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);