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/*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: Edit-Distance based BPM alignment algorithm
*/
#ifndef EDIT_BPM_H_
#define EDIT_BPM_H_
#include "alignment/cigar.h"
#include "system/mm_allocator.h"
typedef struct {
/* BMP Pattern */
char* pattern; // Raw pattern
uint64_t* PEQ; // Pattern equalities (Bit vector for Myers-DP)
uint64_t pattern_length; // Length
uint64_t pattern_num_words64; // ceil(Length / |w|)
uint64_t pattern_mod; // Length % |w|
/* BPM Auxiliary data */
uint64_t* P;
uint64_t* M;
uint64_t* level_mask;
int64_t* score;
int64_t* init_score;
uint64_t* pattern_left;
} bpm_pattern_t;
/*
* BPM matrix
*/
typedef struct {
// Bit-encoded Matrix
uint64_t* Pv;
uint64_t* Mv;
uint64_t min_score;
uint64_t min_score_column;
// CIGAR
cigar_t* cigar;
} bpm_matrix_t;
/*
* Setup
*/
void edit_bpm_pattern_compile(
bpm_pattern_t* const bpm_pattern,
char* const pattern,
const int pattern_length,
mm_allocator_t* const mm_allocator);
void edit_bpm_pattern_free(
bpm_pattern_t* const bpm_pattern,
mm_allocator_t* const mm_allocator);
void edit_bpm_matrix_allocate(
bpm_matrix_t* const bpm_matrix,
const uint64_t pattern_length,
const uint64_t text_length,
mm_allocator_t* const mm_allocator);
void edit_bpm_matrix_free(
bpm_matrix_t* const bpm_matrix,
mm_allocator_t* const mm_allocator);
/*
* Edit distance computation using BPM
*/
void edit_bpm_compute(
bpm_matrix_t* const bpm_matrix,
bpm_pattern_t* const bpm_pattern,
char* const text,
const int text_length,
const int max_distance);
#endif /* EDIT_BPM_H_ */
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