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reverted to the older k_mer_hit definition

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Heng Li
2020-03-27 10:40:31 -04:00
parent 10ed8b36ec
commit 7271c106e4
4 changed files with 40 additions and 48 deletions
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htab.cpp
+12 -8
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@@ -278,7 +278,7 @@ KRADIX_SORT_INIT(ha64, uint64_t, generic_key, 8)
typedef struct {
yak_pt_t *h;
uint64_t n;
uint64_t *a;
ha_idxpos_t *a;
} ha_pt1_t;
struct ha_pt_s {
@@ -340,18 +340,22 @@ int ha_pt_insert_list(ha_pt_t *h, int n, const ha_mz1_t *a)
for (j = 0; j < n; ++j) {
uint64_t x = a[j].x >> h->pre;
khint_t k;
int n;
ha_idxpos_t *p;
if ((a[j].x&mask) != (a[0].x&mask)) continue;
k = yak_pt_get(g->h, x<<YAK_COUNTER_BITS);
if (k == kh_end(g->h)) continue;
assert((kh_key(g->h, k)&YAK_MAX_COUNT) < YAK_MAX_COUNT);
g->a[kh_val(g->h, k) + (kh_key(g->h, k)&YAK_MAX_COUNT)]
= (uint64_t)a[j].rid<<36 | (uint64_t)a[j].rev<<35 | (uint64_t)a[j].pos<<8 | (uint64_t)a[j].span;
n = kh_key(g->h, k) & YAK_MAX_COUNT;
assert(n < YAK_MAX_COUNT);
p = &g->a[kh_val(g->h, k) + n];
p->rid = a[j].rid, p->rev = a[j].rev, p->pos = a[j].pos, p->span = a[j].span;
//(uint64_t)a[j].rid<<36 | (uint64_t)a[j].rev<<35 | (uint64_t)a[j].pos<<8 | (uint64_t)a[j].span;
++kh_key(g->h, k);
++n_ins;
}
return n_ins;
}
/*
static void worker_pt_sort(void *data, long i, int tid)
{
ha_pt_t *h = (ha_pt_t*)data;
@@ -371,7 +375,7 @@ void ha_pt_sort(ha_pt_t *h, int n_thread)
{
kt_for(n_thread, worker_pt_sort, h, 1<<h->pre);
}
*/
void ha_pt_destroy(ha_pt_t *h)
{
int i;
@@ -383,7 +387,7 @@ void ha_pt_destroy(ha_pt_t *h)
free(h->h); free(h);
}
const uint64_t *ha_pt_get(const ha_pt_t *h, uint64_t hash, int *n)
const ha_idxpos_t *ha_pt_get(const ha_pt_t *h, uint64_t hash, int *n)
{
khint_t k;
const ha_pt1_t *g = &h->h[hash & ((1ULL<<h->pre) - 1)];
@@ -799,7 +803,7 @@ ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_f
pt = ha_pt_gen(ct, asm_opt->thread_num);
ha_count(asm_opt, HAF_COUNT_EXACT|HAF_RS_READ, pt, flt_tab, rs);
assert((uint64_t)tot_cnt == pt->tot_pos);
ha_pt_sort(pt, asm_opt->thread_num);
//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);
return pt;