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https://github.com/lh3/minimap2.git
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code refactoring for mm_reg1_t
This commit is contained in:
Heng Li
@@ -0,0 +1,156 @@
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#include <string.h>
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#include <math.h>
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#include "mmpriv.h"
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#include "kalloc.h"
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mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
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{
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mm_reg1_t *r;
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int i, k;
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r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
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for (i = k = 0; i < n_u; ++i) {
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mm_reg1_t *ri = &r[i];
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ri->id = i;
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ri->parent = MM_PARENT_UNSET;
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ri->subsc = 0;
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ri->score = u[i]>>32;
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ri->cnt = (int32_t)u[i];
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ri->as = k;
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mm_reg_set_coor(ri, qlen, a);
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k += ri->cnt;
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}
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return r;
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}
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void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r) // and compute mm_reg1_t::subsc
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{
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int i, j, k, *w;
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if (n <= 0) return;
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w = (int*)kmalloc(km, n * sizeof(int));
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w[0] = 0, r[0].parent = 0;
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for (i = 1, k = 1; i < n; ++i) {
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int si = r[i].qs, ei = r[i].qe;
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for (j = 0; j < k; ++j) {
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int sj = r[w[j]].qs, ej = r[w[j]].qe;
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int min = ej - sj < ei - si? ej - sj : ei - si;
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int ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si);
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if (ol > mask_level * min) {
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r[i].parent = r[w[j]].parent;
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if (r[w[j]].subsc < r[i].score)
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r[w[j]].subsc = r[i].score;
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break;
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}
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}
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if (j == k) w[k++] = i, r[i].parent = i;
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}
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kfree(km, w);
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}
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void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id
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{
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int *tmp, i, max_id = -1, n_tmp;
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if (n_regs <= 0) return;
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for (i = 0; i < n_regs; ++i)
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max_id = max_id > regs[i].id? max_id : regs[i].id;
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n_tmp = max_id + 1;
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tmp = (int*)kmalloc(km, n_tmp * sizeof(int));
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for (i = 0; i < n_tmp; ++i) tmp[i] = -1;
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for (i = 0; i < n_regs; ++i)
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if (regs[i].id >= 0) tmp[regs[i].id] = i;
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for (i = 0; i < n_regs; ++i) {
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mm_reg1_t *r = ®s[i];
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r->id = i;
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if (r->parent == MM_PARENT_TMP_PRI)
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r->parent = i;
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else if (r->parent >= 0 && tmp[r->parent] >= 0)
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r->parent = tmp[r->parent];
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else r->parent = MM_PARENT_UNSET;
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}
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kfree(km, tmp);
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}
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void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r)
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{
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if (pri_ratio > 0.0f && *n_ > 0) {
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int i, k, n = *n_;
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mm_set_parent(km, mask_level, n, r);
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for (i = k = 0; i < n; ++i)
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if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
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r[k++] = r[i];
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if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
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*n_ = k;
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}
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}
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int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
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{ // squeeze out regions in a[] that are not referenced by regs[]
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int i, n_aux, as = 0;
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uint64_t *aux;
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aux = (uint64_t*)kmalloc(km, n_regs * 8);
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for (i = n_aux = 0; i < n_regs; ++i)
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aux[n_aux++] = (uint64_t)regs[i].as << 32 | i;
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for (i = 0; i < n_regs; ++i) {
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mm_reg1_t *r = ®s[i];
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if (r->as != as) {
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memmove(&a[as], &a[r->as], r->cnt * 16);
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r->as = as;
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}
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as += r->cnt;
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}
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kfree(km, aux);
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return as;
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}
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void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a)
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{
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int i, n_aux;
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uint64_t *aux;
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if (n_regs < 2) return; // nothing to join
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mm_squeeze_a(km, n_regs, regs, a);
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aux = (uint64_t*)kmalloc(km, n_regs * 8);
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for (i = n_aux = 0; i < n_regs; ++i)
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if (regs[i].parent == i || regs[i].parent < 0)
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aux[n_aux++] = (uint64_t)regs[i].as << 32 | i;
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radix_sort_64(aux, aux + n_aux);
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for (i = n_aux - 1; i >= 1; --i) {
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mm_reg1_t *r0 = ®s[(int32_t)aux[i-1]], *r1 = ®s[(int32_t)aux[i]];
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mm128_t *a0e, *a1s;
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int max_gap, min_gap;
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// test
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if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
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if (r0->rid != r1->rid || r0->rev != r1->rev) continue; // make sure on the same target and strand
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if (r0->score < opt->min_join_flank_sc || r1->score < opt->min_join_flank_sc) continue; // require good flanking chains
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a0e = &a[r0->as + r0->cnt - 1];
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a1s = &a[r1->as];
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if (a1s->x <= a0e->x || (int32_t)a1s->y <= (int32_t)a0e->y) continue; // keep colinearity
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max_gap = min_gap = (int32_t)a1s->y - (int32_t)a0e->y;
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max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x;
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min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x;
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if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
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// all conditions satisfied; join
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a[r1->as].y |= 1ULL<<40;
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r0->cnt += r1->cnt, r0->score += r1->score;
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mm_reg_set_coor(r0, qlen, a);
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r1->cnt = 0;
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}
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kfree(km, aux);
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}
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void mm_set_mapq(int n_regs, mm_reg1_t *regs)
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{
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int i;
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for (i = 0; i < n_regs; ++i) {
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mm_reg1_t *r = ®s[i];
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if (r->parent == r->id) {
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int mapq;
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mapq = (int)(30.0 * (1. - (float)r->subsc / r->score) * logf(r->score));
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mapq = mapq > 0? mapq : 0;
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r->mapq = mapq < 60? mapq : 60;
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} else r->mapq = 0;
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}
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}
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