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r227: use local alignment for INV alignment

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Heng Li
2017-07-29 17:40:53 -04:00
parent da3db3c095
commit d08b7a0c51
5 changed files with 179 additions and 21 deletions
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align.c
+27 -19
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@@ -357,9 +357,11 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], const mm_reg1_t *r1, const mm_reg1_t *r2, mm_reg1_t *r_inv, ksw_extz_t *ez)
{
int tl, ql, ret = 0;
int tl, ql, score, ret = 0, q_off, t_off;
uint8_t *tseq, *qseq;
int8_t mat[25];
void *qp;
memset(r_inv, 0, sizeof(mm_reg1_t));
if (!(r1->split&1) || !(r2->split&2)) return 0;
if (r1->id != r1->parent && r1->parent != MM_PARENT_TMP_PRI) return 0;
@@ -369,28 +371,34 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
tl = r2->rs - r1->re;
if (ql < 0 || ql > opt->max_gap) return 0;
if (tl < 0 || tl > opt->max_gap) return 0;
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
tseq = (uint8_t*)kmalloc(km, tl);
mm_idx_getseq(mi, r1->rid, r1->re, r2->rs, tseq);
qseq = &qseq0[!r1->rev][qlen - r2->qs];
mm_align_pair(km, opt, ql, qseq, tl, tseq, mat, (int)(opt->bw * 1.5), KSW_EZ_APPROX_MAX, ez);
if (ez->n_cigar > 0 && ez->score > 0) {
mm_append_cigar(r_inv, ez->n_cigar, ez->cigar);
r_inv->p->dp_score = ez->score;
mm_update_extra(r_inv->p, qseq, tseq, mat, opt->q, opt->e);
if (r_inv->p->dp_max < opt->min_dp_max) { // discard this hit
free(r_inv->p);
r_inv->p = 0;
} else {
r_inv->id = -1;
r_inv->parent = MM_PARENT_UNSET;
r_inv->inv = 1;
r_inv->rev = !r1->rev;
r_inv->qs = r1->qe, r_inv->qe = r2->qs;
r_inv->rs = r1->re, r_inv->re = r2->rs;
ret = 1;
}
}
mm_seq_rev(ql, qseq);
mm_seq_rev(tl, tseq);
qp = ksw_ll_qinit(km, 2, ql, qseq, 5, mat);
score = ksw_ll_i16(qp, tl, tseq, opt->q, opt->e, &q_off, &t_off);
kfree(km, qp);
mm_seq_rev(ql, qseq);
mm_seq_rev(tl, tseq);
if (score < opt->min_dp_max) goto end_align1_inv;
q_off = ql - (q_off + 1), t_off = tl - (t_off + 1);
mm_align_pair(km, opt, ql - q_off, qseq + q_off, tl - t_off, tseq + t_off, mat, (int)(opt->bw * 1.5), KSW_EZ_EXTZ_ONLY, ez);
if (ez->n_cigar == 0) goto end_align1_inv; // should never be here
mm_append_cigar(r_inv, ez->n_cigar, ez->cigar);
r_inv->p->dp_score = ez->max;
mm_update_extra(r_inv->p, qseq + q_off, tseq + t_off, mat, opt->q, opt->e);
r_inv->id = -1;
r_inv->parent = MM_PARENT_UNSET;
r_inv->inv = 1;
r_inv->rev = !r1->rev;
r_inv->qs = r1->qe + q_off, r_inv->qe = r_inv->qs + ez->max_q + 1;
r_inv->rs = r1->re + t_off, r_inv->re = r_inv->rs + ez->max_t + 1;
ret = 1;
end_align1_inv:
kfree(km, tseq);
return ret;
}