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validate z-drop

This commit is contained in:
Heng Li 2017-06-27 11:25:39 -04:00
parent c02ff4662c
commit 734028f92b
1 changed files with 36 additions and 1 deletions
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37
align.c
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@ -41,6 +41,41 @@ static void mm_reg_split(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *
r->split = r2->split = 1;
}
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)
{
if (score < *max) {
int li = i - *max_i;
int lj = j - *max_j;
int diff = li > lj? li - lj : lj - li;
if (*max - score > zdrop + diff * e)
return 1;
} else *max = score, *max_i = i, *max_j = j;
return 0;
}
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)
{
uint32_t k;
int32_t score = 0, max = 0, max_i = -1, max_j = -1, i = 0, j = 0;
for (k = 0; k < n_cigar; ++k) {
uint32_t l, op = cigar[k]&0xf, len = cigar[k]>>4;
if (op == 0) {
for (l = 0; l < len; ++l) {
score += mat[tseq[i + l] * 5 + qseq[j + l]];
if (test_zdrop_aux(score, i+l, j+l, &max, &max_i, &max_j, e, zdrop)) return 1;
}
i += len, j += len;
} else if (op == 1) {
score -= q + e * len, j += len;
if (test_zdrop_aux(score, i, j, &max, &max_i, &max_j, e, zdrop)) return 1;
} else if (op == 2) {
score -= q + e * len, i += len;
if (test_zdrop_aux(score, i, j, &max, &max_i, &max_j, e, zdrop)) return 1;
}
}
return 0;
}
static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, uint32_t n_cigar, uint32_t *cigar, int rev_cigar)
{
uint32_t l, toff = 0, qoff = 0;
@ -189,7 +224,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, KSW_EZ_GLOBAL_ONLY, ez);
if (ez->zdropped || ez->score < 0)
if (ez->zdropped || ez->score < 0 || mm_check_zdrop(qseq, tseq, ez->n_cigar, ez->cigar, mat, opt->q, opt->e, opt->zdrop))
ksw_extz2_sse(km, qe - qs, qseq, re - rs, tseq, 5, mat, opt->q, opt->e, bw, opt->zdrop, 0, ez);
if (ez->n_cigar > 0) {
mm_append_cigar(r, ez->n_cigar, ez->cigar);