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
135
136
137
138
139
140
141
142
143
144
145
146
147
|
/*
* 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>
*/
#ifndef ALIGN_BENCHMARK_PARAMS_H_
#define ALIGN_BENCHMARK_PARAMS_H_
#include "utils/commons.h"
#include "benchmark/benchmark_utils.h"
/*
* Algorithms
*/
typedef enum {
// Test
alignment_test,
// Indel
alignment_indel_wavefront,
// Edit
alignment_edit_bpm,
alignment_edit_dp,
alignment_edit_dp_banded,
alignment_edit_wavefront,
// Gap-linear
alignment_gap_linear_nw,
alignment_gap_linear_wavefront,
// Gap-affine
alignment_gap_affine_swg,
alignment_gap_affine_swg_endsfree,
alignment_gap_affine_swg_banded,
alignment_gap_affine_wavefront,
// Gap-affine dual-cost
alignment_gap_affine2p_dp,
alignment_gap_affine2p_wavefront,
} alignment_algorithm_type;
/*
* Match function
*/
typedef struct {
char* pattern;
int pattern_length;
char* text;
int text_length;
} match_function_params_t;
extern match_function_params_t match_function_params;
/*
* Align-benchmark Parameters
*/
typedef struct {
// Algorithm
alignment_algorithm_type algorithm;
// I/O
char *input_filename;
char *output_filename;
bool output_full;
// I/O internals
FILE* input_file;
char* line1;
char* line2;
size_t line1_allocated;
size_t line2_allocated;
FILE* output_file;
// Penalties
linear_penalties_t linear_penalties;
affine_penalties_t affine_penalties;
affine2p_penalties_t affine2p_penalties;
// Alignment form
bool endsfree;
double pattern_begin_free;
double text_begin_free;
double pattern_end_free;
double text_end_free;
// Wavefront parameters
bool wfa_score_only;
wf_heuristic_strategy wfa_heuristic;
int wfa_heuristic_p1;
int wfa_heuristic_p2;
int wfa_heuristic_p3;
wavefront_memory_t wfa_memory_mode;
alignment_match_funct_t wfa_match_funct;
void* wfa_match_funct_arguments;
uint64_t wfa_max_memory;
int wfa_max_score;
int wfa_max_threads;
// Other algorithms parameters
int bandwidth;
// Misc
bool check_display;
bool check_correct;
bool check_score;
bool check_alignments;
int check_metric;
int check_bandwidth;
int plot;
// Profile
profiler_timer_t timer_global;
// System
int num_threads;
int batch_size;
int progress;
int verbose;
} align_bench_params_t;
// Defaults
extern align_bench_params_t parameters;
/*
* Menu
*/
void usage();
/*
* Parse arguments
*/
void parse_arguments(
int argc,
char** argv);
#endif /* ALIGN_BENCHMARK_PARAMS_H_ */
|
