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r326: select high-occ k-mers (experimental)

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Heng Li
2020-10-29 22:36:54 -04:00
parent f37c4e29fa
commit f02eb66e6a
4 changed files with 59 additions and 20 deletions
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htab.cpp
+7 -6
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@@ -189,7 +189,7 @@ static int ha_ct_insert_list(ha_ct_t *h, int create_new, int n, const uint64_t *
///so low 12 bits are not useful
uint64_t x = a[j] >> h->pre;
khint_t k;
if ((a[j]&mask) != (a[0]&mask)) continue;
assert((a[j]&mask) == (a[0]&mask));
if (create_new) {
///for 0-th counting, g->b = NULL
if (g->b)
@@ -365,9 +365,9 @@ int ha_pt_insert_list(ha_pt_t *h, int n, const ha_mz1_t *a)
khint_t k;
int n;
ha_idxpos_t *p;
if ((a[j].x&mask) != (a[0].x&mask)) continue;
assert((a[j].x&mask) == (a[0].x&mask));
k = yak_pt_get(g->h, x<<YAK_COUNTER_BITS);
if (k == kh_end(g->h)) continue;
if (k == kh_end(g->h)) continue; // TODO: understand why we sometimes come here
n = kh_key(g->h, k) & YAK_MAX_COUNT;
assert(n < YAK_MAX_COUNT);
p = &g->a[kh_val(g->h, k) + n];
@@ -518,7 +518,7 @@ typedef struct { // global data structure for kt_pipeline()
const yak_copt_t *opt;
const void *flt_tab;
int flag, create_new, is_store;
uint64_t n_seq; ///number of total reads
uint64_t n_mz, n_seq; ///number of total reads
kseq_t *ks;
UC_Read ucr;
ha_ct_t *ct;
@@ -573,8 +573,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
s->n_seq0 = p->n_seq;
if (p->rs_in && (p->flag & HAF_RS_READ)) {
while (p->n_seq < p->rs_in->total_reads) {
if((p->flag & HAF_SKIP_READ) && p->rs_in->trio_flag[p->n_seq] != AMBIGU)
{
if ((p->flag & HAF_SKIP_READ) && p->rs_in->trio_flag[p->n_seq] != AMBIGU) {
++p->n_seq;
continue;
}
@@ -685,6 +684,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
ct_insert_buf(s->buf, p->opt->pre, s->mz[i].a[j].x);
}
for (i = 0; i < s->n_seq; ++i) {
p->n_mz += s->mz[i].n;
free(s->mz[i].a);
if (!p->is_store) free(s->seq[i]);
}
@@ -763,6 +763,7 @@ static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt
gzclose(fp);
}
*n_seq = pl.n_seq;
if (pl.opt->w > 1) fprintf(stderr, "[M::%s] collected %ld minimizers\n", __func__, (long)pl.n_mz);
return pl.ct;
}