miniwfa.h

/*
  The MIT License

  Copyright (c) 2022-     Dana-Farber Cancer Institute

  Permission is hereby granted, free of charge, to any person obtaining
  a copy of this software and associated documentation files (the
  "Software"), to deal in the Software without restriction, including
  without limitation the rights to use, copy, modify, merge, publish,
  distribute, sublicense, and/or sell copies of the Software, and to
  permit persons to whom the Software is furnished to do so, subject to
  the following conditions:

  The above copyright notice and this permission notice shall be
  included in all copies or substantial portions of the Software.

  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
  BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
  ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.
*/

#ifndef MINIWFA_H
#define MINIWFA_H

#include <stdint.h>

#define MWF_F_CIGAR      0x1
#define MWF_F_NO_KALLOC  0x2
#define MWF_F_DEBUG      0x10000

typedef struct {
	int32_t flag;     // bit flag; see MWF_F_* macros
	int32_t x, o1, e1, o2, e2; // scoring
	int32_t step;     // distance between checkpoints in the low-memory mode
	int32_t max_s;    // stop the alignment if score is higher than this
	int64_t max_iter;
	// chaining heuristics
	int32_t max_occ, kmer, min_len;
} mwf_opt_t;

typedef struct {
	int32_t s;       // score
	int32_t n_cigar; // number of CIGAR operators
	int64_t n_iter;
	uint32_t *cigar; // CIGAR in the htslib packing: len<<4|op
} mwf_rst_t;

#ifdef __cplusplus
extern "C" {
#endif

/**
 * Set default parameters
 *
 * @param opt     (out) options
 */
void mwf_opt_init(mwf_opt_t *opt);

/**
 * Align two sequences with WFA
 *
 * mwf_wfa_exact() finds the optimal alignment without heuristics.
 *
 * mwf_wfa_chain() does chaining and closes gaps in the chain. This is a
 * heuristic algorithm and may miss the optimal alignment.
 *
 * mwf_wfa_auto() calls mwf_wfa_exact() for penalty up to 5000. If fails,
 * it invokes mwf_wfa_chain() with a step size of 5000.
 *
 * @param km      kalloc handler. Set to NULL to use malloc.
 * @param opt     parameters
 * @param tl      target sequence length
 * @param ts      target sequence
 * @param ql      query sequence length
 * @param qs      query sequence
 * @param r       (out) results
 */
void mwf_wfa_exact(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);
void mwf_wfa_chain(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);
void mwf_wfa_auto(void *km, const mwf_opt_t *opt,  int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);

// These functions are in "mwf-dbg.c". For debugging only.
int32_t mwf_cigar2score(const mwf_opt_t *opt, int32_t n_cigar, const uint32_t *cigar, int32_t *tl, int32_t *ql);
void mwf_assert_cigar(const mwf_opt_t *opt, int32_t n_cigar, const uint32_t *cigar, int32_t tl0, int32_t ql0, int32_t s0);

#ifdef __cplusplus
}
#endif

#endif