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r495: fix impropriate CIGAR

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1. Not left aligned
2. In one case, 50M24D50M becomes 24D100M. The leading D needs to be removed.
3. Avoid identical hits after DP
This commit is contained in:
Heng Li
2017-10-10 11:59:44 -04:00
parent 46fa520db9
commit 13b66aad4d
3 changed files with 71 additions and 10 deletions
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align.c
+61 -4
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@@ -62,11 +62,68 @@ static int mm_check_zdrop(const uint8_t *qseq, const uint8_t *tseq, uint32_t n_c
return 0;
}
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)
static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq, int *qshift, int *tshift)
{
mm_extra_t *p = r->p;
int32_t k, toff = 0, qoff = 0, to_shrink = 0;
*qshift = *tshift = 0;
if (p->n_cigar <= 1) return;
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;
if (op == 0) {
toff += len, qoff += len;
} else if (op == 1 || op == 2) { // insertion or deletion
if (k > 0 && k < p->n_cigar - 1 && (p->cigar[k-1]&0xf) == 0 && (p->cigar[k+1]&0xf) == 0) {
int l, prev_len = p->cigar[k-1] >> 4;
if (op == 1) {
for (l = 0; l < prev_len; ++l)
if (qseq[qoff - 1 - l] != qseq[qoff + len - 1 - l])
break;
} else {
for (l = 0; l < prev_len; ++l)
if (tseq[toff - 1 - l] != tseq[toff + len - 1 - l])
break;
}
if (l > 0)
p->cigar[k-1] -= l<<4, p->cigar[k+1] += l<<4, qoff -= l, toff -= l;
if (l == prev_len) to_shrink = 1;
}
if (op == 1) qoff += len;
else toff += len;
} else if (op == 3) {
toff += len;
}
}
assert(qoff == r->qe - r->qs && toff == r->re - r->rs);
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
if (p->cigar[k]>>4 != 0)
p->cigar[l++] = p->cigar[k];
p->n_cigar = l;
for (k = l = 0; k < p->n_cigar; ++k) // merge two adjacent operations if they are the same
if (k == p->n_cigar - 1 || (p->cigar[k]&0xf) != (p->cigar[k+1]&0xf))
p->cigar[l++] = p->cigar[k];
p->n_cigar = l;
}
if ((p->cigar[0]&0xf) == 1 || (p->cigar[0]&0xf) == 2) { // get rid of leading I or D
int32_t l = p->cigar[0] >> 4;
if ((p->cigar[0]&0xf) == 1) r->qs += l, *qshift = l;
else r->rs += l, *tshift = l;
--p->n_cigar;
memmove(p->cigar, p->cigar + 1, p->n_cigar * 4);
}
}
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)
{
uint32_t k, l, toff = 0, qoff = 0;
int32_t s = 0, max = 0;
int32_t s = 0, max = 0, qshift, tshift;
mm_extra_t *p = r->p;
if (p == 0) return;
mm_fix_cigar(r, qseq, tseq, &qshift, &tshift);
qseq += qshift, tseq += tshift; // qseq and tseq may be shifted due to the removal of leading I/D
for (k = 0; k < p->n_cigar; ++k) {
uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
if (op == 0) { // match/mismatch
@@ -424,7 +481,7 @@ 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) {
mm_idx_getseq(mi, rid, rs1, re1, tseq);
mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e);
mm_update_extra(r, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e);
if (rev && r->p->trans_strand)
r->p->trans_strand ^= 3; // flip to the read strand
}
@@ -467,7 +524,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
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);
mm_update_extra(r_inv, 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;