#ifndef KSW2_H_ #define KSW2_H_ #include #define KSW_NEG_INF -0x40000000 #define KSW_EZ_SCORE_ONLY 0x01 // don't record alignment path/cigar #define KSW_EZ_RIGHT 0x02 // right-align gaps #define KSW_EZ_GENERIC_SC 0x04 // without this flag: match/mismatch only; last symbol is a wildcard #define KSW_EZ_APPROX_MAX 0x08 // approximate max; this is faster with sse #define KSW_EZ_APPROX_DROP 0x10 // approximate Z-drop; faster with sse #define KSW_EZ_EXTZ_ONLY 0x40 // only perform extension #define KSW_EZ_REV_CIGAR 0x80 // reverse CIGAR in the output #define KSW_EZ_SPLICE_FOR 0x100 #define KSW_EZ_SPLICE_REV 0x200 #define KSW_EZ_SPLICE_FLANK 0x400 // The subset of CIGAR operators used by ksw code. // Use MM_CIGAR_* from minimap.h if you need the full list. #define KSW_CIGAR_MATCH 0 #define KSW_CIGAR_INS 1 #define KSW_CIGAR_DEL 2 #define KSW_CIGAR_N_SKIP 3 #ifdef __cplusplus extern "C" { #endif typedef struct { 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 int m_cigar, n_cigar; int reach_end; uint32_t *cigar; } ksw_extz_t; /** * NW-like extension * * @param km memory pool, when used with kalloc * @param qlen query length * @param query query sequence with 0 <= query[i] < m * @param tlen target length * @param target target sequence with 0 <= target[i] < m * @param m number of residue types * @param mat m*m scoring mattrix in one-dimension array * @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)" * @param gape gap extension penalty * @param w band width (<0 to disable) * @param zdrop off-diagonal drop-off to stop extension (positive; <0 to disable) * @param flag flag (see KSW_EZ_* macros) * @param ez (out) scores and cigar */ void ksw_extz(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int flag, ksw_extz_t *ez); void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez); void ksw_extd(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int flag, ksw_extz_t *ez); void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez); void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int8_t junc_bonus, int flag, const uint8_t *junc, ksw_extz_t *ez); void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez); /** * Global alignment * * (first 10 parameters identical to ksw_extz_sse()) * @param m_cigar (modified) max CIGAR length; feed 0 if cigar==0 * @param n_cigar (out) number of CIGAR elements * @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, ) * * @return score of the alignment */ int ksw_gg(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_); int ksw_gg2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_); int ksw_gg2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_); void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, const int8_t *mat); int ksw_ll_i16(void *q, int tlen, const uint8_t *target, int gapo, int gape, int *qe, int *te); #ifdef __cplusplus } #endif /************************************ *** Private macros and functions *** ************************************/ #ifdef HAVE_KALLOC #include "kalloc.h" #else #include #define kmalloc(km, size) malloc((size)) #define kcalloc(km, count, size) calloc((count), (size)) #define krealloc(km, ptr, size) realloc((ptr), (size)) #define kfree(km, ptr) free((ptr)) #endif static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint32_t op, int len) { if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) { if (*n_cigar == *m_cigar) { *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2); } cigar[(*n_cigar)++] = len<<4 | op; } else cigar[(*n_cigar)-1] += len<<4; return cigar; } // In the backtrack matrix, value p[] has the following structure: // bit 0-2: which type gets the max - 0 for H, 1 for E, 2 for F, 3 for \tilde{E} and 4 for \tilde{F} // bit 3/0x08: 1 if a continuation on the E state (bit 5/0x20 for a continuation on \tilde{E}) // bit 4/0x10: 1 if a continuation on the F state (bit 6/0x40 for a continuation on \tilde{F}) static inline void ksw_backtrack(void *km, int is_rot, int is_rev, int min_intron_len, const uint8_t *p, const int *off, const int *off_end, int n_col, int i0, int j0, int *m_cigar_, int *n_cigar_, uint32_t **cigar_) { // p[] - lower 3 bits: which type gets the max; bit int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; uint32_t *cigar = *cigar_, tmp; while (i >= 0 && j >= 0) { // at the beginning of the loop, _state_ tells us which state to check int force_state = -1; if (is_rot) { r = i + j; if (i < off[r]) force_state = 2; if (off_end && i > off_end[r]) force_state = 1; tmp = force_state < 0? p[(size_t)r * n_col + i - off[r]] : 0; } else { if (j < off[i]) force_state = 2; if (off_end && j > off_end[i]) force_state = 1; tmp = force_state < 0? p[(size_t)i * n_col + j - off[i]] : 0; } if (state == 0) state = tmp & 7; // if requesting the H state, find state one maximizes it. else if (!(tmp >> (state + 2) & 1)) state = 0; // if requesting other states, _state_ stays the same if it is a continuation; otherwise, set to H if (state == 0) state = tmp & 7; // TODO: probably this line can be merged into the "else if" line right above; not 100% sure if (force_state >= 0) state = force_state; if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_MATCH, 1), --i, --j; else if (state == 1 || (state == 3 && min_intron_len <= 0)) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_DEL, 1), --i; else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_N_SKIP, 1), --i; else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, 1), --j; } if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, min_intron_len > 0 && i >= min_intron_len? KSW_CIGAR_N_SKIP : KSW_CIGAR_DEL, i + 1); // first deletion if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, j + 1); // first insertion if (!is_rev) for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp; *m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar; } static inline void ksw_reset_extz(ksw_extz_t *ez) { 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, ez->reach_end = 0; } static inline int ksw_apply_zdrop(ksw_extz_t *ez, int is_rot, int32_t H, int a, int b, int zdrop, int8_t e) { int r, t; if (is_rot) r = a, t = b; else r = a + b, t = a; if (H > (int32_t)ez->max) { ez->max = H, ez->max_t = t, ez->max_q = r - t; } else if (t >= ez->max_t && r - t >= ez->max_q) { int tl = t - ez->max_t, ql = (r - t) - ez->max_q, l; l = tl > ql? tl - ql : ql - tl; if (zdrop >= 0 && ez->max - H > zdrop + l * e) { ez->zdropped = 1; return 1; } } return 0; } #endif