170 lines
7.7 KiB
C
170 lines
7.7 KiB
C
#ifndef KSW2_H_
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#define KSW2_H_
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#include <stdint.h>
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#define KSW_NEG_INF -0x40000000
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#define KSW_EZ_SCORE_ONLY 0x01 // don't record alignment path/cigar
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#define KSW_EZ_RIGHT 0x02 // right-align gaps
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#define KSW_EZ_GENERIC_SC 0x04 // without this flag: match/mismatch only; last symbol is a wildcard
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#define KSW_EZ_APPROX_MAX 0x08 // approximate max; this is faster with sse
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#define KSW_EZ_APPROX_DROP 0x10 // approximate Z-drop; faster with sse
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#define KSW_EZ_EXTZ_ONLY 0x40 // only perform extension
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#define KSW_EZ_REV_CIGAR 0x80 // reverse CIGAR in the output
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#ifdef __cplusplus
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extern "C" {
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#endif
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typedef struct {
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uint32_t max:31, zdropped:1;
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int max_q, max_t; // max extension coordinate
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int mqe, mqe_t; // max score when reaching the end of query
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int mte, mte_q; // max score when reaching the end of target
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int score; // max score reaching both ends; may be KSW_NEG_INF
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int m_cigar, n_cigar;
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uint32_t *cigar;
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} ksw_extz_t;
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/**
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* NW-like extension
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*
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* @param km memory pool, when used with kalloc
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* @param qlen query length
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* @param query query sequence with 0 <= query[i] < m
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* @param tlen target length
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* @param target target sequence with 0 <= target[i] < m
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* @param m number of residue types
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* @param mat m*m scoring mattrix in one-dimension array
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* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
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* @param gape gap extension penalty
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* @param w band width (<0 to disable)
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* @param zdrop off-diagonal drop-off to stop extension (positive; <0 to disable)
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* @param flag flag (see KSW_EZ_* macros)
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* @param ez (out) scores and cigar
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*/
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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);
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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 flag, ksw_extz_t *ez);
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void ksw_extd(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
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int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int flag, ksw_extz_t *ez);
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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,
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int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int flag, ksw_extz_t *ez);
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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,
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int8_t gapo, int8_t gape, int8_t gapo2, int zdrop, int flag, ksw_extz_t *ez);
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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);
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/**
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* Global alignment
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*
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* (first 10 parameters identical to ksw_extz_sse())
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* @param m_cigar (modified) max CIGAR length; feed 0 if cigar==0
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* @param n_cigar (out) number of CIGAR elements
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* @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
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*
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* @return score of the alignment
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*/
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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_);
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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_);
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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_);
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void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, const int8_t *mat);
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int ksw_ll_i16(void *q, int tlen, const uint8_t *target, int gapo, int gape, int *qe, int *te);
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#ifdef __cplusplus
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}
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#endif
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/************************************
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*** Private macros and functions ***
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************************************/
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#ifdef HAVE_KALLOC
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#include "kalloc.h"
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#else
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#include <stdlib.h>
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#define kmalloc(km, size) malloc((size))
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#define kcalloc(km, count, size) calloc((count), (size))
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#define krealloc(km, ptr, size) realloc((ptr), (size))
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#define kfree(km, ptr) free((ptr))
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#endif
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static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint32_t op, int len)
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{
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if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
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if (*n_cigar == *m_cigar) {
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*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
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cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2);
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}
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cigar[(*n_cigar)++] = len<<4 | op;
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} else cigar[(*n_cigar)-1] += len<<4;
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return cigar;
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}
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// In the backtrack matrix, value p[] has the following structure:
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// 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}
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// bit 3/0x08: 1 if a continuation on the E state (bit 5/0x20 for a continuation on \tilde{E})
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// bit 4/0x10: 1 if a continuation on the F state (bit 6/0x40 for a continuation on \tilde{F})
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static inline void ksw_backtrack(void *km, int is_rot, int is_rev, 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_)
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{ // p[] - lower 3 bits: which type gets the max; bit
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int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0;
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uint32_t *cigar = *cigar_, tmp;
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while (i >= 0 && j >= 0) { // at the beginning of the loop, _state_ tells us which state to check
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int force_state = -1;
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if (is_rot) {
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r = i + j;
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if (i < off[r]) force_state = 2;
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if (off_end && i > off_end[r]) force_state = 1;
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tmp = force_state < 0? p[r * n_col + i - off[r]] : 0;
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} else {
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if (j < off[i]) force_state = 2;
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if (off_end && j > off_end[i]) force_state = 1;
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tmp = force_state < 0? p[i * n_col + j - off[i]] : 0;
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}
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if (state == 0) state = tmp & 7; // if requesting the H state, find state one maximizes it.
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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
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if (state == 0) state = tmp & 7; // TODO: probably this line can be merged into the "else if" line right above; not 100% sure
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if (force_state >= 0) state = force_state;
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if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
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else if (state == 1 || state == 3) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
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else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
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}
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if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
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if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
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if (!is_rev)
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for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
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tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
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*m_cigar_ = m_cigar, *n_cigar_ = n_cigar, *cigar_ = cigar;
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}
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static inline void ksw_reset_extz(ksw_extz_t *ez)
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{
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ez->max_q = ez->max_t = ez->mqe_t = ez->mte_q = -1;
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ez->max = 0, ez->score = ez->mqe = ez->mte = KSW_NEG_INF;
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ez->n_cigar = 0, ez->zdropped = 0;
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}
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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)
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{
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int r, t;
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if (is_rot) r = a, t = b;
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else r = a + b, t = a;
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if (H > (int32_t)ez->max) {
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ez->max = H, ez->max_t = t, ez->max_q = r - t;
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} else if (t >= ez->max_t && r - t >= ez->max_q) {
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int tl = t - ez->max_t, ql = (r - t) - ez->max_q, l;
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l = tl > ql? tl - ql : ql - tl;
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if (zdrop >= 0 && ez->max - H > zdrop + l * e) {
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ez->zdropped = 1;
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return 1;
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}
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}
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return 0;
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}
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#endif
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