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r93: fixed various small issues

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Heng Li
2017-06-28 10:35:21 -04:00
parent cdc2a1e29f
commit bcd9b1c621
4 changed files with 64 additions and 23 deletions
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map.c
+7 -7
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@@ -15,16 +15,17 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->sdust_thres = 0;
opt->min_cnt = 3;
opt->min_score = 40;
opt->min_chain_score = 40;
opt->bw = 1000;
opt->max_gap = 10000;
opt->max_skip = 15;
opt->max_chain_skip = 15;
opt->pri_ratio = 2.0f;
opt->mask_level = 0.5f;
opt->a = 1, opt->b = 1, opt->q = 1, opt->e = 1;
opt->zdrop = 100;
opt->min_dp_score = 0;
opt->min_ksw_len = 100;
}
@@ -165,6 +166,7 @@ mm_reg1_t *mm_gen_reg(int qlen, int n_u, uint64_t *u, mm128_t *a)
r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
for (i = k = 0; i < n_u; ++i) {
mm_reg1_t *ri = &r[i];
ri->id = i;
ri->parent = -1, ri->subsc = 0;
ri->score = u[i]>>32;
ri->cnt = (int32_t)u[i];
@@ -210,11 +212,12 @@ void mm_select_sub(float mask_level, float pri_ratio, int *n_, mm_reg1_t *r, voi
if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
tmp[i] = k, r[k++] = r[i];
n = k;
for (i = 0; i < n; ++i)
for (i = 0; i < n; ++i) // remap mm_reg1_t::parent, as some mappings may have been dropped
if (tmp[r[i].parent] >= 0)
r[i].parent = tmp[r[i].parent];
kfree(km, tmp);
*n_ = n;
for (i = 0; i < n; ++i) r[i].id = i; // reset mm_reg1_t::id
}
}
@@ -286,9 +289,8 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
for (i = 0; i < n; ++i)
if (m[i].is_alloc) kfree(b->km, m[i].x.r);
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_cnt, opt->min_score, n_a, a, &u, b->km);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_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);
@@ -371,8 +373,6 @@ static void *worker_pipeline(void *shared, int step, void *in)
bseq1_t *t = &s->seq[i];
for (j = 0; j < s->n_reg[i]; ++j) {
mm_reg1_t *r = &s->reg[i][j];
if (r->p && r->p->blen - r->p->n_ambi - r->p->n_diff < p->opt->min_score)
continue;
if (p->opt->flag & MM_F_OUT_SAM) mm_write_sam(&p->str, mi, t, j, r);
else mm_write_paf(&p->str, mi, t, j, r);
puts(p->str.s);