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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: Benchmark utils
*/
#ifndef BENCHMARK_UTILS_H_
#define BENCHMARK_UTILS_H_
#include "utils/commons.h"
#include "system/mm_allocator.h"
#include "system/profiler_timer.h"
#include "alignment/score_matrix.h"
#include "wavefront/wavefront_aligner.h"
/*
* Constants
*/
#define ALIGN_DEBUG_CHECK_CORRECT 0x00000001
#define ALIGN_DEBUG_CHECK_SCORE 0x00000002
#define ALIGN_DEBUG_CHECK_ALIGNMENT 0x00000004
#define ALIGN_DEBUG_DISPLAY_INFO 0x00000008
#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_INDEL 0x00000010
#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_EDIT 0x00000040
#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAR 0x00000080
#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE 0x00000100
#define ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE2P 0x00000400
/*
* Alignment Input
*/
typedef struct {
// Sequences
int sequence_id;
char* pattern;
int pattern_length;
char* text;
int text_length;
// Penalties
linear_penalties_t linear_penalties;
affine_penalties_t affine_penalties;
affine2p_penalties_t affine2p_penalties;
// Alignment form
bool ends_free;
int pattern_begin_free;
int text_begin_free;
int pattern_end_free;
int text_end_free;
// Output
FILE* output_file;
bool output_full;
// MM
wavefront_aligner_t* wf_aligner;
mm_allocator_t* mm_allocator;
// PROFILE/STATS
profiler_timer_t timer;
profiler_counter_t align;
profiler_counter_t align_correct;
profiler_counter_t align_score;
profiler_counter_t align_score_total;
profiler_counter_t align_score_diff;
profiler_counter_t align_cigar;
profiler_counter_t align_bases;
profiler_counter_t align_matches;
profiler_counter_t align_mismatches;
profiler_counter_t align_del;
profiler_counter_t align_ins;
// DEBUG
int debug_flags;
linear_penalties_t* check_linear_penalties;
affine_penalties_t* check_affine_penalties;
affine2p_penalties_t* check_affine2p_penalties;
int check_bandwidth;
bool verbose;
} align_input_t;
/*
* Setup
*/
void benchmark_align_input_clear(
align_input_t* const align_input);
/*
* Display
*/
void benchmark_print_alignment(
FILE* const stream,
align_input_t* const align_input,
const int score_computed,
cigar_t* const cigar_computed,
const int score_correct,
cigar_t* const cigar_correct);
void benchmark_print_output(
align_input_t* const align_input,
const distance_metric_t distance_metric,
const bool score_only,
cigar_t* const cigar);
/*
* Stats
*/
void benchmark_print_stats(
FILE* const stream,
align_input_t* const align_input,
const bool print_wf_stats);
#endif /* BENCHMARK_UTILS_H_ */
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