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r85: two-round z-drop

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Heng Li
2017-06-27 10:36:24 -04:00
parent 490a37a599
commit c02ff4662c
4 changed files with 39 additions and 35 deletions
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ksw2.h
+6 -18
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@@ -14,7 +14,8 @@
#define KSW_EZ_REV_CIGAR 0x40 // reverse CIGAR in the output
typedef struct {
int max, max_q, max_t; // max extension score and coordinate
uint32_t max:31, zdropped:1;
int max_q, max_t; // max extension coordinate
int mqe, mqe_t; // max score when reaching the end of query
int mte, mte_q; // max score when reaching the end of target
int score; // max score reaching both ends; may be KSW_NEG_INF
@@ -112,24 +113,11 @@ static inline void ksw_backtrack(void *km, int is_rot, int is_rev, const uint8_t
*m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar;
}
static inline int ksw_cigar2score(int8_t m, const int8_t *mat, int8_t q, int8_t e, const uint8_t *query, const uint8_t *target, int n_cigar, const uint32_t *cigar)
static inline void ksw_reset_extz(ksw_extz_t *ez)
{
int i, j, k, l, score;
for (k = 0, score = 0, i = j = 0; k < n_cigar; ++k) {
int op = cigar[k] & 0xf, len = cigar[k] >> 4;
if (op == 0) {
for (l = 0; l < len; ++l)
score += mat[target[i + l] * m + query[j + l]];
i += len, j += len;
} else if (op == 1) {
score -= q + len * e;
j += len;
} else if (op == 2) {
score -= q + len * e;
i += len;
}
}
return score;
ez->max_q = ez->max_t = ez->mqe_t = ez->mte_q = -1;
ez->max = 0, ez->score = ez->mqe = ez->mte = KSW_NEG_INF;
ez->n_cigar = 0, ez->zdropped = 0;
}
#endif