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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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lchain.c
+1 -2
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@@ -251,7 +251,7 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
{
int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
int64_t *p, i, i0, st = 0, st_inner = 0, n_iter = 0;
int64_t *p, i, i0, st = 0, st_inner = 0;
uint64_t *u;
lc_elem_t *root = 0, *root_inner = 0;
void *mem_mp = 0;
@@ -345,7 +345,6 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
}
if (!krmq_itr_prev(lc_elem, &itr)) break;
}
n_iter += n_rmq_iter;
}
}
}