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r89: added minimal number of minimizer counts

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Heng Li
2017-06-27 18:43:15 -04:00
parent 8977f07269
commit fa80177e58
5 changed files with 19 additions and 11 deletions
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map.c
+3 -2
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@@ -14,8 +14,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->mid_occ_frac = 2e-4f;
opt->sdust_thres = 0;
opt->min_cnt = 3;
opt->min_score = 40;
opt->bw = 1000;
opt->bw = 10000;
opt->max_gap = 10000;
opt->max_skip = 15;
@@ -286,7 +287,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
kfree(b->km, m);
//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x, (uint32_t)a[i].y);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_score, n_a, a, &u, b->km);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_cnt, opt->min_score, n_a, a, &u, b->km);
regs = mm_gen_reg(qlen, n_u, u, a);
*n_regs = n_u;
mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);