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
|
// Copyright (c) 2020 Robert Vaser
#ifndef BIOPARSER_FASTA_PARSER_HPP_
#define BIOPARSER_FASTA_PARSER_HPP_
#include <cstdint>
#include <memory>
#include <vector>
#include <stdexcept>
#include <string>
#include "bioparser/parser.hpp"
namespace bioparser {
template<class T>
class FastaParser: public Parser<T> {
public:
FastaParser(const FastaParser&) = delete;
FastaParser& operator=(const FastaParser&) = delete;
FastaParser(FastaParser&&) = delete;
FastaParser& operator=(FastaParser&&) = delete;
~FastaParser() {}
std::vector<std::unique_ptr<T>> Parse(
std::uint64_t bytes, bool shorten_names = true) override {
std::vector<std::unique_ptr<T>> dst;
std::uint64_t parsed_bytes = 0;
std::uint32_t data_ptr = 0;
auto create_T = [&] () -> void {
if (data_ptr == 0) {
throw std::invalid_argument(
"[bioparser::FastaParser] error: invalid file format");
}
auto name_len = shorten_names ?
this->Shorten(this->storage().data(), data_ptr) :
this->RightStrip(this->storage().data(), data_ptr);
auto data_len = this->storage_ptr() - data_ptr;
if (name_len == 0 || this->storage()[0] != '>' || data_len == 0) {
throw std::invalid_argument(
"[bioparser::FastaParser] error: invalid file format");
}
dst.emplace_back(std::unique_ptr<T>(new T(
static_cast<const char*>(this->storage().data() + 1), name_len - 1,
static_cast<const char*>(this->storage().data() + data_ptr), data_len))); // NOLINT
parsed_bytes += this->storage_ptr();
data_ptr = 0;
this->Clear();
};
bool is_eof = false;
bool is_name = true;
while (true) {
auto buffer_ptr = this->buffer_ptr();
for (; buffer_ptr < this->buffer_bytes(); ++buffer_ptr) {
auto c = this->buffer()[buffer_ptr];
if (c == '\n') {
this->Store(buffer_ptr - this->buffer_ptr(), !is_name);
if (is_name) {
data_ptr = this->storage_ptr();
is_name = false;
}
} else if (!is_name && c == '>') {
is_name = true;
create_T();
if (parsed_bytes >= bytes) {
return dst;
}
}
}
if (this->buffer_ptr() < buffer_ptr) {
this->Store(buffer_ptr - this->buffer_ptr(), !is_name);
}
if (is_eof) {
break;
}
is_eof = this->Read();
}
if (this->storage_ptr() != 0) {
create_T();
}
return dst;
}
private:
explicit FastaParser(gzFile file)
: Parser<T>(file, 4194304) {} // 4 MB
friend Parser<T>;
};
} // namespace bioparser
#endif // BIOPARSER_FASTA_PARSER_HPP_
|
