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
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
|
# Bioparser
[](https://github.com/rvaser/bioparser/releases/latest)
Bioparser is a c++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
## Build
### Dependencies
- gcc 4.8+ | clang 3.5+
- zlib 1.2.8+
#### Hidden
- (bioparser_test) rvaser/biosoup 0.11.0
- (bioparser_test) google/googletest 1.10.0
### CMake (3.11+)
```bash
git clone https://github.com/rvaser/bioparser && cd bioparser
cmake -B build -DCMAKE_BUILD_TYPE=Release
make -C build
```
#### Options
- `bioparser_install`: generate install target
- `bioparser_build_tests`: build unit tests
### Meson (0.60.0+)
```bash
git clone https://github.com/rvaser/bioparser && cd bioparser
meson setup build
ninja -C build
```
#### Options
- `tests`: build unit tests
## Examples
#### FASTA parser
```cpp
#include "bioparser/fasta_parser.hpp"
struct Sequence { // or any other name
public:
Sequence( // required arguments
const char*, std::uint32_t,
const char*, std::uint32_t) {
// implementation
}
}
auto p = bioparser::Parser<Sequence>::Create<bioparser::FastaParser>(path);
// parse whole file
auto s = p->Parse(-1);
```
#### FASTQ parser
```cpp
#include "bioparser/fastq_parser.hpp"
struct Sequence { // or any other name
public:
Sequence( // required arguments
const char*, std::uint32_t,
const char*, std::uint32_t,
const char*, std::uint32_t) {
// implementation
}
}
auto p = bioparser::Parser<Sequence>::Create<bioparser::FastqParser>(path);
// parse in chunks
std::vector<std::unique_ptr<Sequence>> s;
while (true) {
auto c = p->Parse(1ULL << 30); // 1 GB
if (c.empty()) {
break;
}
s.insert(
s.end(),
std::make_move_iterator(c.begin()),
std::make_move_iterator(c.end()));
}
```
#### MHAP parser
```cpp
#include "bioparser/mhap_parser.hpp"
struct Overlap { // or any other name
public:
Overlap( // required arguments
std::uint64_t,
std::uint64_t,
double error,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t) {
// implementation
}
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::MhapParser>(path);
// parse whole file
auto o = p->Parse(-1);
```
#### PAF parser
```cpp
#include "bioparser/paf_parser.hpp"
struct Overlap { // or any other name
public:
Overlap( // required arguments
const char*, std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
char,
const char*, std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t,
std::uint32_t) {
// implementation
}
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::PafParser>(path);
// parse whole file
auto o = p->Parse(-1);
```
#### SAM parser
```cpp
#include "bioparser/sam_parser.hpp"
struct Overlap { // or any other name
public:
Overlap( // required arguments
const char*, std::uint32_t,
std::uint32_t,
const char*, std::uint32_t,
std::uint32_t,
std::uint32_t,
const char*, std::uint32_t,
const char*, std::uint32_t,
std::uint32_t,
std::uint32_t,
const char*, std::uint32_t,
const char*, std::uint32_t) {
// implementation
}
}
auto p = bioparser::Parser<Overlap>::Create<bioparser::SamParser>(path);
// parse whole file
auto o = p->Parse(-1);
```
**Note**: If your class has a private constructor, add one of the following lines to your class definition:
```cpp
friend bioparser::FastaParser<Sequence>;
friend bioparser::FastqParser<Sequence>;
friend bioparser::MhapParser<Overlap>;
friend bioparser::PafParser<Overlap>;
friend bioparser::SamParser<Overlap>;
```
## Acknowledgement
This work has been supported in part by the Croatian Science Foundation under the project Single genome and metagenome assembly (IP-2018-01-5886).
|
