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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* 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.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: Cigar data-structure (match/mismatch/insertion/deletion)
*/
#ifndef CIGAR_H_
#define CIGAR_H_
#include "system/mm_allocator.h"
#include "alignment/linear_penalties.h"
#include "alignment/affine_penalties.h"
#include "alignment/affine2p_penalties.h"
/*
* CIGAR
*/
typedef struct {
// Operations buffer
char* operations;
int max_operations;
int begin_offset;
int end_offset;
// Score
int score;
// MM
mm_allocator_t* mm_allocator;
} cigar_t;
/*
* Setup
*/
cigar_t* cigar_new(
const int max_operations,
mm_allocator_t* const mm_allocator);
void cigar_clear(
cigar_t* const cigar);
void cigar_resize(
cigar_t* const cigar,
const int max_operations);
void cigar_free(
cigar_t* const cigar);
/*
* Accessors
*/
int cigar_get_matches(
cigar_t* const cigar);
void cigar_add_mismatches(
char* const pattern,
const int pattern_length,
char* const text,
const int text_length,
cigar_t* const cigar);
/*
* Score
*/
int cigar_score_edit(
cigar_t* const cigar);
int cigar_score_gap_linear(
cigar_t* const cigar,
linear_penalties_t* const penalties);
int cigar_score_gap_affine(
cigar_t* const cigar,
affine_penalties_t* const penalties);
int cigar_score_gap_affine2p(
cigar_t* const cigar,
affine2p_penalties_t* const penalties);
/*
* Utils
*/
int cigar_cmp(
cigar_t* const cigar_a,
cigar_t* const cigar_b);
void cigar_copy(
cigar_t* const cigar_dst,
cigar_t* const cigar_src);
void cigar_append(
cigar_t* const cigar_dst,
cigar_t* const cigar_src);
void cigar_append_deletion(
cigar_t* const cigar,
const int length);
void cigar_append_insertion(
cigar_t* const cigar,
const int length);
bool cigar_check_alignment(
FILE* const stream,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
cigar_t* const cigar,
const bool verbose);
/*
* Display
*/
void cigar_print(
FILE* const stream,
cigar_t* const cigar,
const bool print_matches);
int cigar_sprint(
char* buffer,
cigar_t* const cigar,
const bool print_matches);
void cigar_print_pretty(
FILE* const stream,
const char* const pattern,
const int pattern_length,
const char* const text,
const int text_length,
cigar_t* const cigar,
mm_allocator_t* const mm_allocator);
#endif /* CIGAR_H_ */
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