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
|
// Copyright (c) 2020 Robert Vaser
#include "bioparser/fasta_parser.hpp"
#include <numeric>
#include "biosoup/sequence.hpp"
#include "gtest/gtest.h"
#include "bioparser_test_config.h"
std::atomic<std::uint32_t> biosoup::Sequence::num_objects{0};
namespace bioparser {
namespace test {
class BioparserFastaTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
p = Parser<biosoup::Sequence>::Create<FastaParser>(BIOPARSER_TEST_DATA + file);
}
void Check(bool is_trimmed = true) {
EXPECT_EQ(14, s.size());
EXPECT_EQ(65 + !is_trimmed * 10, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->name.size();
}));
EXPECT_EQ(109117, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->data.size();
}));
EXPECT_EQ(0, std::accumulate(s.begin(), s.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<biosoup::Sequence>& it) {
return s + it->quality.size();
}));
}
std::unique_ptr<Parser<biosoup::Sequence>> p;
std::vector<std::unique_ptr<biosoup::Sequence>> s;
};
TEST_F(BioparserFastaTest, ParseWhole) {
Setup("sample.fasta");
s = p->Parse(-1);
Check();
}
TEST_F(BioparserFastaTest, ParseWholeWithoutTrimming) {
Setup("sample.fasta");
s = p->Parse(-1, false);
Check(false);
}
TEST_F(BioparserFastaTest, ParseInChunks) {
Setup("sample.fasta");
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastaTest, FormatError) {
Setup("sample.fastq");
try {
s = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::FastaParser] error: invalid file format");
}
}
TEST_F(BioparserFastaTest, ParseAndReset) {
Setup("sample.fasta");
s = p->Parse(-1);
p->Reset();
s.clear();
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastaTest, CompressedParseWhole) {
Setup("sample.fasta.gz");
s = p->Parse(-1);
Check();
}
TEST_F(BioparserFastaTest, CompressedParseWholeWithoutTrimming) {
Setup("sample.fasta.gz");
s = p->Parse(-1, false);
Check(false);
}
TEST_F(BioparserFastaTest, CompressedParseInChunks) {
Setup("sample.fasta.gz");
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastaTest, CompressedParseAndReset) {
Setup("sample.fasta.gz");
s = p->Parse(-1);
p->Reset();
s.clear();
for (auto t = p->Parse(65536); !t.empty(); t = p->Parse(65536)) {
s.insert(
s.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserFastaTest, CompressedFormatError) {
Setup("sample.fastq.gz");
try {
s = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::FastaParser] error: invalid file format");
}
}
} // namespace test
} // namespace bioparser
|
