ksw2.h

#ifndef KSW2_H_
#define KSW2_H_

#include <stdint.h>

#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
#define KSW_EZ_SPLICE_CMPLX 0x800  // use the miniprot splice model
#define KSW_EZ_SPLICE_SCORE 0x1000 // use splice score

// 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

#define KSW_SPSC_OFFSET  64

#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, int end_bonus, int8_t junc_bonus, int8_t junc_pen, 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 <stdlib.h>
#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