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working on toy examples

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This commit is contained in:
Heng Li
2018-09-17 13:54:57 -04:00
parent d01369ec47
commit edf736e110
4 changed files with 47 additions and 31 deletions
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13
align.c
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@@ -88,13 +88,14 @@ static int mm_test_zdrop(void *km, const mm_mapopt_t *opt, const uint8_t *qseq,
return max_zdrop > opt->zdrop? 1 : 0;
}
static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, int *qshift, int *tshift)
static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, int *qshift, int *tshift, int left_aln)
{
mm_extra_t *p = r->p;
int32_t toff = 0, qoff = 0, to_shrink = 0;
uint32_t k;
*qshift = *tshift = 0;
if (p->n_cigar <= 1) return;
if (!left_aln) goto end_left_aln;
for (k = 0; k < p->n_cigar; ++k) { // indel left alignment
uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
if (len == 0) to_shrink = 1;
@@ -123,6 +124,7 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
}
}
assert(qoff == r->qe - r->qs && toff == r->re - r->rs);
end_left_aln:
if (to_shrink) { // squeeze out zero-length operations
int32_t l = 0;
for (k = 0; k < p->n_cigar; ++k) // squeeze out zero-length operations
@@ -147,13 +149,13 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
}
}
static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e)
static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e, int left_aln)
{
uint32_t k, l;
int32_t s = 0, max = 0, qshift, tshift, toff = 0, qoff = 0;
mm_extra_t *p = r->p;
if (p == 0) return;
mm_fix_cigar(r, qseq, tseq, &qshift, &tshift);
mm_fix_cigar(r, qseq, tseq, &qshift, &tshift, left_aln);
qseq += qshift, tseq += tshift; // qseq and tseq may be shifted due to the removal of leading I/D
r->blen = r->mlen = 0;
for (k = 0; k < p->n_cigar; ++k) {
@@ -748,8 +750,9 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(re1 - rs1 <= re0 - rs0);
if (r->p) {
int left_aln = (opt->flag & MM_F_SPLICE) || mi->n_R == 0? 1 : 0;
mm_idx_getseq2(mi, rid, rs1, re1, tseq, ob);
mm_update_extra(r, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e);
mm_update_extra(r, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, left_aln);
if (opt->flag & MM_F_EQX) mm_update_cigar_eqx(r, &qseq0[r->rev][qs1], tseq);
if (rev && r->p->trans_strand)
r->p->trans_strand ^= 3; // flip to the read strand
@@ -809,7 +812,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
}
r_inv->rs = r1->re + t_off;
r_inv->re = r_inv->rs + ez->max_t + 1;
mm_update_extra(r_inv, &qseq[q_off], &tseq[t_off], mat, opt->q, opt->e);
mm_update_extra(r_inv, &qseq[q_off], &tseq[t_off], mat, opt->q, opt->e, 0);
if (opt->flag & MM_F_EQX) mm_update_cigar_eqx(r_inv, &qseq[q_off], &tseq[t_off]);
ret = 1;
end_align1_inv: