314 lines
9.8 KiB
C
314 lines
9.8 KiB
C
#include <assert.h>
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#include <string.h>
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#include "minimap.h"
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#include "mmpriv.h"
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#include "ksw2.h"
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static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
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{
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int i, j;
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a = a < 0? -a : a;
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b = b > 0? -b : b;
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for (i = 0; i < m - 1; ++i) {
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for (j = 0; j < m - 1; ++j)
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mat[i * m + j] = i == j? a : b;
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mat[i * m + m - 1] = 0;
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}
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for (j = 0; j < m; ++j)
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mat[(m - 1) * m + j] = 0;
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}
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static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
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{
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uint32_t i;
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uint8_t t;
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for (i = 0; i < len>>1; ++i)
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t = seq[i], seq[i] = seq[len - 1 - i], seq[len - 1 - i] = t;
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}
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static inline int test_zdrop_aux(int32_t score, int i, int j, int32_t *max, int *max_i, int *max_j, int e, int zdrop)
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{
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if (score < *max) {
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int li = i - *max_i;
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int lj = j - *max_j;
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int diff = li > lj? li - lj : lj - li;
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if (*max - score > zdrop + diff * e)
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return 1;
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} else *max = score, *max_i = i, *max_j = j;
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return 0;
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}
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static int mm_check_zdrop(const uint8_t *qseq, const uint8_t *tseq, uint32_t n_cigar, uint32_t *cigar, const int8_t *mat, int8_t q, int8_t e, int zdrop)
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{
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uint32_t k;
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int32_t score = 0, max = 0, max_i = -1, max_j = -1, i = 0, j = 0;
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for (k = 0; k < n_cigar; ++k) {
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uint32_t l, op = cigar[k]&0xf, len = cigar[k]>>4;
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if (op == 0) {
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for (l = 0; l < len; ++l) {
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score += mat[tseq[i + l] * 5 + qseq[j + l]];
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if (test_zdrop_aux(score, i+l, j+l, &max, &max_i, &max_j, e, zdrop)) return 1;
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}
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i += len, j += len;
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} else if (op == 1) {
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score -= q + e * len, j += len;
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if (test_zdrop_aux(score, i, j, &max, &max_i, &max_j, e, zdrop)) return 1;
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} else if (op == 2) {
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score -= q + e * len, i += len;
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if (test_zdrop_aux(score, i, j, &max, &max_i, &max_j, e, zdrop)) return 1;
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}
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}
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return 0;
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}
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static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e)
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{
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uint32_t k, l, toff = 0, qoff = 0;
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int32_t s = 0, max = 0;
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if (p == 0) return;
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for (k = 0; k < p->n_cigar; ++k) {
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uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
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if (op == 0) {
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for (l = 0; l < len; ++l) {
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int cq = qseq[qoff + l], ct = tseq[toff + l];
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if (ct > 3 || cq > 3) ++p->n_ambi;
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else if (ct != cq) ++p->n_diff;
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s += mat[ct * 5 + cq];
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if (s < 0) s = 0;
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else max = max > s? max : s;
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}
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toff += len, qoff += len, p->blen += len;
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} else if (op == 1) {
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int n_ambi = 0;
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for (l = 0; l < len; ++l)
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if (qseq[qoff + l] > 3) ++n_ambi;
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qoff += len, p->blen += len;
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p->n_ambi += n_ambi, p->n_diff += len - n_ambi;
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s -= q + e * len;
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if (s < 0) s = 0;
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} else if (op == 2) {
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int n_ambi = 0;
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for (l = 0; l < len; ++l)
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if (tseq[toff + l] > 3) ++n_ambi;
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toff += len, p->blen += len;
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p->n_ambi += n_ambi, p->n_diff += len - n_ambi;
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s -= q + e * len;
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if (s < 0) s = 0;
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}
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}
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p->dp_max = max;
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}
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static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
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{
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mm_extra_t *p;
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if (n_cigar == 0) return;
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if (r->p == 0) {
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uint32_t capacity = n_cigar + sizeof(mm_extra_t);
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kroundup32(capacity);
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r->p = (mm_extra_t*)calloc(capacity, 4);
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r->p->capacity = capacity;
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} else if (r->p->n_cigar + n_cigar + sizeof(mm_extra_t) > r->p->capacity) {
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r->p->capacity = r->p->n_cigar + n_cigar + sizeof(mm_extra_t);
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kroundup32(r->p->capacity);
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r->p = (mm_extra_t*)realloc(r->p, r->p->capacity * 4);
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}
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p = r->p;
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if (p->n_cigar > 0 && (p->cigar[p->n_cigar-1]&0xf) == (cigar[0]&0xf)) { // same CIGAR op at the boundary
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p->cigar[p->n_cigar-1] += cigar[0]>>4<<4;
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if (n_cigar > 1) memcpy(p->cigar + p->n_cigar, cigar + 1, (n_cigar - 1) * 4);
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p->n_cigar += n_cigar - 1;
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} else {
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memcpy(p->cigar + p->n_cigar, cigar, n_cigar * 4);
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p->n_cigar += n_cigar;
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}
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}
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static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const int8_t *mat, int w, int flag, ksw_extz_t *ez)
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{
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if (opt->q == opt->q2 && opt->e == opt->e2)
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ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, opt->zdrop, flag, ez);
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else
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ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, opt->zdrop, flag, ez);
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}
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static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x)
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{
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int64_t i, off0 = mi->seq[rid].offset, off = off0 + x;
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int c = mm_seq4_get(mi->S, off);
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for (i = off - 1; i >= off0; --i)
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if (mm_seq4_get(mi->S, i) != c) break;
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return (int)(off - i);
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}
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static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2], mm128_t *a, int32_t *r, int32_t *q)
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{
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if (mi->is_hpc) {
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const uint8_t *qseq = qseq0[a->x>>63];
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int i, c;
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*q = (int32_t)a->y;
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for (i = *q - 1, c = qseq[*q]; i > 0; --i)
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if (qseq[i] != c) break;
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*q = i + 1;
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c = mm_get_hplen_back(mi, a->x<<1>>33, (int32_t)a->x);
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*r = (int32_t)a->x + 1 - c;
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} else {
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*r = (int32_t)a->x + 1;
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*q = (int32_t)a->y + 1;
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}
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}
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static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
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{
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int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
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uint8_t *tseq, *qseq;
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int32_t i, l, bw, dropped = 0, rs0, re0, qs0, qe0;
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int32_t rs, re, qs, qe;
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int32_t rs1, qs1, re1, qe1;
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int8_t mat[25];
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if (r->cnt == 0) return;
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ksw_gen_simple_mat(5, mat, opt->a, opt->b);
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bw = (int)(opt->bw * 1.5 + 1.);
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r2->cnt = 0;
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mm_adjust_minier(mi, qseq0, &a[r->as], &rs, &qs);
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mm_adjust_minier(mi, qseq0, &a[r->as + r->cnt - 1], &re, &qe);
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// compute rs0 and qs0
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if (r->split && r->as > 0) {
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mm_adjust_minier(mi, qseq0, &a[r->as-1], &rs0, &qs0);
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} else {
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if (qs > 0 && rs > 0) { // actually this is always true
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l = qs < opt->max_gap? qs : opt->max_gap;
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qs0 = qs - l;
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l += l * opt->a > opt->q? (l * opt->a - opt->q) / opt->e : 0;
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l = l < opt->max_gap? l : opt->max_gap;
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l = l < rs? l : rs;
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rs0 = rs - l;
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} else rs0 = rs, qs0 = qs;
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}
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// compute re0 and qe0
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if (qe < qlen && re < mi->seq[rid].len) {
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l = qlen - qe < opt->max_gap? qlen - qe : opt->max_gap;
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qe0 = qe + l;
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l += l * opt->a > opt->q? (l * opt->a - opt->q) / opt->e : 0;
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l = l < opt->max_gap? l : opt->max_gap;
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l = l < mi->seq[rid].len - re? l : mi->seq[rid].len - re;
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re0 = re + l;
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} else re0 = re, qe0 = qe;
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assert(re0 > rs0);
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tseq = (uint8_t*)kmalloc(km, re0 - rs0);
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if (qs > 0 && rs > 0) { // left extension
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qseq = &qseq0[rev][qs0];
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mm_idx_getseq(mi, rid, rs0, rs, tseq);
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mm_seq_rev(qs - qs0, qseq);
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mm_seq_rev(rs - rs0, tseq);
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mm_align_pair(km, opt, qs - qs0, qseq, rs - rs0, tseq, mat, bw, KSW_EZ_EXTZ_ONLY|KSW_EZ_RIGHT|KSW_EZ_REV_CIGAR, ez);
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if (ez->n_cigar > 0) {
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mm_append_cigar(r, ez->n_cigar, ez->cigar);
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r->p->dp_score += ez->max;
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}
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rs1 = rs - (ez->max_t + 1);
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qs1 = qs - (ez->max_q + 1);
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mm_seq_rev(qs - qs0, qseq);
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} else rs1 = rs, qs1 = qs;
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re1 = rs, qe1 = qs;
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assert(qs1 >= 0 && rs1 >= 0);
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for (i = 1; i < r->cnt; ++i) { // gap filling
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mm_adjust_minier(mi, qseq0, &a[r->as + i], &re, &qe);
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re1 = re, qe1 = qe;
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if (i == r->cnt - 1 || (a[r->as+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
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int bw1 = bw;
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if (a[r->as+i].y>>40&1)
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bw1 = qe - qs > re - rs? qe - qs : re - rs;
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qseq = &qseq0[rev][qs];
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mm_idx_getseq(mi, rid, rs, re, tseq);
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mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, mat, bw1, KSW_EZ_APPROX_MAX, ez);
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if (mm_check_zdrop(qseq, tseq, ez->n_cigar, ez->cigar, mat, opt->q, opt->e, opt->zdrop))
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mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, mat, bw1, 0, ez);
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if (ez->n_cigar > 0)
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mm_append_cigar(r, ez->n_cigar, ez->cigar);
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if (ez->zdropped) { // truncated by Z-drop; TODO: sometimes Z-drop kicks in because the next seed placement is wrong. This can be fixed in principle.
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int j;
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for (j = i - 1; j >= 0; --j)
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if ((int32_t)a[r->as + j].x < re + ez->max_t)
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break;
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dropped = 1;
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r->p->dp_score += ez->max;
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re1 = rs + (ez->max_t + 1);
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qe1 = qs + (ez->max_q + 1);
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if (r->cnt - (j + 1) >= opt->min_cnt)
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mm_split_reg(r, r2, j + 1, qlen, a);
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break;
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} else r->p->dp_score += ez->score;
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rs = re, qs = qe;
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}
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}
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if (!dropped && qe < qe0 && re < re0) { // right extension
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qseq = &qseq0[rev][qe];
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mm_idx_getseq(mi, rid, re, re0, tseq);
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mm_align_pair(km, opt, qe0 - qe, qseq, re0 - re, tseq, mat, bw, KSW_EZ_EXTZ_ONLY, ez);
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if (ez->n_cigar > 0) {
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mm_append_cigar(r, ez->n_cigar, ez->cigar);
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r->p->dp_score += ez->max;
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}
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re1 = re + (ez->max_t + 1);
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qe1 = qe + (ez->max_q + 1);
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}
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assert(qe1 <= qlen);
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r->rs = rs1, r->re = re1;
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if (rev) r->qs = qlen - qe1, r->qe = qlen - qs1;
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else r->qs = qs1, r->qe = qe1;
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assert(re1 - rs1 <= re0 - rs0);
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if (r->p) {
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mm_idx_getseq(mi, rid, rs1, re1, tseq);
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mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e);
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}
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kfree(km, tseq);
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}
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mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
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{
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extern unsigned char seq_nt4_table[256];
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int32_t i, r, n_regs = *n_regs_;
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uint8_t *qseq0[2];
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ksw_extz_t ez;
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// encode the query sequence
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qseq0[0] = (uint8_t*)kmalloc(km, qlen);
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qseq0[1] = (uint8_t*)kmalloc(km, qlen);
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for (i = 0; i < qlen; ++i) {
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qseq0[0][i] = seq_nt4_table[(uint8_t)qstr[i]];
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qseq0[1][qlen - 1 - i] = qseq0[0][i] < 4? 3 - qseq0[0][i] : 4;
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}
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// align through seed hits
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memset(&ez, 0, sizeof(ksw_extz_t));
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for (r = 0; r < n_regs; ++r) {
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mm_reg1_t r2;
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mm_align1(km, opt, mi, qlen, qseq0, ®s[r], &r2, a, &ez);
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if (r2.cnt > 0) {
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regs = (mm_reg1_t*)realloc(regs, (n_regs + 1) * sizeof(mm_reg1_t)); // this should be very rare
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if (r + 1 != n_regs)
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memmove(®s[r + 2], ®s[r + 1], sizeof(mm_reg1_t) * (n_regs - r - 1));
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regs[r + 1] = r2;
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++n_regs;
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}
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}
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*n_regs_ = n_regs;
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kfree(km, qseq0[0]); kfree(km, qseq0[1]);
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kfree(km, ez.cigar);
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mm_filter_regs(km, opt, n_regs_, regs);
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mm_hit_sort_by_dp(km, n_regs_, regs);
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return regs;
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}
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