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dev-r1076: log gap penalty

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Heng Li
2021-07-17 18:23:59 -04:00
parent 52fafe0fed
commit 2546999639
5 changed files with 27 additions and 20 deletions
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align.c
+10 -7
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@@ -237,10 +237,11 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
r->p = p;
}
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 is_eqx)
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 is_eqx, int log_gap)
{
uint32_t k, l;
int32_t s = 0, max = 0, qshift, tshift, toff = 0, qoff = 0;
int32_t qshift, tshift, toff = 0, qoff = 0;
double s = 0.0, max = 0.0;
mm_extra_t *p = r->p;
if (p == 0) return;
mm_fix_cigar(r, qseq, tseq, &qshift, &tshift);
@@ -265,7 +266,8 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
for (l = 0; l < len; ++l)
if (qseq[qoff + l] > 3) ++n_ambi;
r->blen += len - n_ambi, p->n_ambi += n_ambi;
s -= q + e * len;
if (log_gap) s -= q + (double)e * mg_log2(1.0 + len);
else s -= q + e * len;
if (s < 0) s = 0;
qoff += len;
} else if (op == MM_CIGAR_DEL) {
@@ -273,14 +275,15 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
for (l = 0; l < len; ++l)
if (tseq[toff + l] > 3) ++n_ambi;
r->blen += len - n_ambi, p->n_ambi += n_ambi;
s -= q + e * len;
if (log_gap) s -= q + (double)e * mg_log2(1.0 + len);
else s -= q + e * len;
if (s < 0) s = 0;
toff += len;
} else if (op == MM_CIGAR_N_SKIP) {
toff += len;
}
}
p->dp_max = max;
p->dp_max = (int32_t)(max + .499);
assert(qoff == r->qe - r->qs && toff == r->re - r->rs);
if (is_eqx) mm_update_cigar_eqx(r, qseq, tseq); // NB: it has to be called here as changes to qseq and tseq are not returned
}
@@ -813,7 +816,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_idx_getseq(mi, rid, rs1, re1, tseq);
qseq = &qseq0[r->rev][qs1];
}
mm_update_extra(r, qseq, tseq, mat, opt->q, opt->e, opt->flag & MM_F_EQX);
mm_update_extra(r, qseq, tseq, mat, opt->q, opt->e, opt->flag & MM_F_EQX, !(opt->flag&MM_F_NO_LOG_GAP));
if (rev && r->p->trans_strand)
r->p->trans_strand ^= 3; // flip to the read strand
}
@@ -872,7 +875,7 @@ 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, opt->flag & MM_F_EQX);
mm_update_extra(r_inv, &qseq[q_off], &tseq[t_off], mat, opt->q, opt->e, opt->flag & MM_F_EQX, !(opt->flag&MM_F_NO_LOG_GAP));
ret = 1;
end_align1_inv:
kfree(km, tseq);