libwfa2 0.1.1

Bindings to the C implementation of WFA2-lib
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134

/*
 *                             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;
  alignment_match_funct_t wfa_match_funct;
  void* wfa_match_funct_arguments;
  // Penalties
  linear_penalties_t linear_penalties;
  affine_penalties_t affine_penalties;
  affine2p_penalties_t affine2p_penalties;
  // Alignment form
  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_ */