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r1149: implemented random open syncmer

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On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher
accuracy. The speed becomes a little slower. There seems a benefit but not a
big one.
This commit is contained in:
Heng Li
2022-10-21 19:07:28 -04:00
parent cefd0d9f6c
commit c2f07ff2ac
9 changed files with 84 additions and 8 deletions
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index.c
+2 -2
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@@ -358,7 +358,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
for (i = 0; i < s->n_seq; ++i) {
mm_bseq1_t *t = &s->seq[i];
if (t->l_seq > 0)
mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, &s->a);
mm_sketch2(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, p->mi->flag&MM_I_SYNCMER, &s->a);
else if (mm_verbose >= 2)
fprintf(stderr, "[WARNING] the length database sequence '%s' is 0\n", t->name);
free(t->seq); free(t->name);
@@ -446,7 +446,7 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
sum_len += p->len;
if (p->len > 0) {
a.n = 0;
mm_sketch(0, s, p->len, w, k, i, is_hpc, &a);
mm_sketch2(0, s, p->len, w, k, i, is_hpc, 0, &a); // TODO: mm_idx_str() doesn't support syncmer
mm_idx_add(mi, a.n, a.a);
}
}