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
|
// Copyright (c) 2020 Robert Vaser
#include "bioparser/sam_parser.hpp"
#include <numeric>
#include <string>
#include "biosoup/overlap.hpp"
#include "gtest/gtest.h"
#include "bioparser_test_config.h"
namespace bioparser {
namespace test {
struct SamOverlap: public biosoup::Overlap {
public:
SamOverlap(
const char* q_name, std::uint32_t q_name_len,
std::uint32_t flag,
const char* t_name, std::uint32_t t_name_len,
std::uint32_t t_begin,
std::uint32_t map_quality,
const char* cigar, std::uint32_t cigar_len,
const char* t_next_name, std::uint32_t t_next_name_len,
std::uint32_t t_next_begin,
std::uint32_t template_len,
const char* data, std::uint32_t data_len,
const char* quality, std::uint32_t quality_len)
: biosoup::Overlap(
0, 0, 0,
0, t_begin, 0,
0,
cigar, cigar_len),
q_name(q_name, q_name_len),
flag(flag),
t_name(t_name, t_name_len),
map_quality(map_quality),
t_next_name(t_next_name, t_next_name_len),
t_next_begin(t_next_begin),
template_len(template_len),
data(data, data_len),
quality(quality, quality_len) {}
std::string q_name;
std::uint32_t flag;
std::string t_name;
std::uint32_t map_quality;
std::string t_next_name;
std::uint32_t t_next_begin;
std::uint32_t template_len;
std::string data;
std::string quality;
};
class BioparserSamTest: public ::testing::Test {
public:
void Setup(const std::string& file) {
p = Parser<SamOverlap>::Create<SamParser>(BIOPARSER_TEST_DATA + file);
}
void Check() {
EXPECT_EQ(48, o.size());
EXPECT_EQ(795237, std::accumulate(o.begin(), o.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<SamOverlap>& it) {
return s +
it->q_name.size() +
it->t_name.size() +
it->alignment.size() +
it->t_next_name.size() +
it->data.size() +
it->quality.size();
}));
EXPECT_EQ(639677, std::accumulate(o.begin(), o.end(), 0,
[] (std::uint32_t s, const std::unique_ptr<SamOverlap>& it) {
return s +
it->flag +
it->rhs_begin +
it->map_quality +
it->t_next_begin +
it->template_len;
}));
}
std::unique_ptr<Parser<SamOverlap>> p;
std::vector<std::unique_ptr<SamOverlap>> o;
};
TEST_F(BioparserSamTest, ParseWhole) {
Setup("sample.sam");
o = p->Parse(-1);
Check();
}
TEST_F(BioparserSamTest, ParseInChunks) {
Setup("sample.sam");
for (auto t = p->Parse(1024); !t.empty(); t = p->Parse(1024)) {
o.insert(
o.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserSamTest, FormatError) {
Setup("sample.paf");
try {
o = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::SamParser] error: invalid file format");
}
}
TEST_F(BioparserSamTest, CompressedParseWhole) {
Setup("sample.sam.gz");
o = p->Parse(-1);
Check();
}
TEST_F(BioparserSamTest, CompressedParseInChunks) {
Setup("sample.sam.gz");
for (auto t = p->Parse(1024); !t.empty(); t = p->Parse(1024)) {
o.insert(
o.end(),
std::make_move_iterator(t.begin()),
std::make_move_iterator(t.end()));
}
Check();
}
TEST_F(BioparserSamTest, CompressedFormatError) {
Setup("sample.paf.gz");
try {
o = p->Parse(-1);
} catch (std::invalid_argument& exception) {
EXPECT_STREQ(
exception.what(),
"[bioparser::SamParser] error: invalid file format");
}
}
} // namespace test
} // namespace bioparser
|
