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
|
// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#include <gtest/gtest.h>
#include <iostream>
#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
#include <seqan3/core/debug_stream/byte.hpp>
#include <seqan3/core/debug_stream/optional.hpp>
#include <seqan3/core/debug_stream/tuple.hpp>
#include <seqan3/core/debug_stream/variant.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/fixture/io/sequence_file/standard_fixture.hpp>
#include <seqan3/test/pretty_printing.hpp>
using sequence_file_seek_test_fixture = std::tuple<std::filesystem::path /*sequence_file_path*/,
bool /*has_base_qualities*/,
std::vector<std::streampos> /*file_positions*/>;
struct sequence_file_seek_test : public ::testing::TestWithParam<sequence_file_seek_test_fixture>
{
void SetUp() override
{
std::tie(sequence_file_path, has_base_qualities, file_positions) = GetParam();
sequence_file_path = std::filesystem::path{CURRENT_SOURCE_DIR} / sequence_file_path;
}
template <typename record_t, typename expected_record_t>
void expect_record_eq(record_t & record, expected_record_t & expected_record)
{
EXPECT_EQ(record.sequence(), expected_record.sequence());
EXPECT_EQ(record.id(), expected_record.id());
if (has_base_qualities)
{
EXPECT_EQ(record.base_qualities(), expected_record.base_qualities());
}
}
std::filesystem::path sequence_file_path;
bool has_base_qualities;
std::vector<std::streampos> file_positions;
};
TEST_P(sequence_file_seek_test, seek_to)
{
seqan3::test::fixture::io::sequence_file::standard_fixture expected_file{};
seqan3::sequence_file_input fin{sequence_file_path};
ASSERT_GE(expected_file.records.size(), 3u);
auto it = fin.begin();
for (size_t i = 0u; i < expected_file.records.size(); ++it, ++i)
{
SCOPED_TRACE("sequential access");
ASSERT_EQ(it.file_position(), file_positions[i]);
expect_record_eq(*it, expected_file.records[i]);
EXPECT_TRUE(it != fin.end());
}
EXPECT_TRUE(it == fin.end());
for (size_t i : std::vector<size_t>{2u, 1u, 0u, 1u, 0u, 2u, 0u, 0u, 2u, 2u, 1u, 1u})
{
SCOPED_TRACE("random access");
it.seek_to(file_positions[i]);
expect_record_eq(*it, expected_file.records[i]);
EXPECT_TRUE(it != fin.end());
}
EXPECT_TRUE(it != fin.end());
for (size_t i = 1u; i < expected_file.records.size(); ++it, ++i)
{
SCOPED_TRACE("finish access sequentially");
expect_record_eq(*it, expected_file.records[i]);
EXPECT_TRUE(it != fin.end());
}
EXPECT_TRUE(it == fin.end());
}
sequence_file_seek_test_fixture fasta_file_fixture{"standard.fasta", false, {0, 25, 114}};
INSTANTIATE_TEST_SUITE_P(fasta_file, sequence_file_seek_test, ::testing::Values(fasta_file_fixture));
sequence_file_seek_test_fixture fastq_file_fixture{"standard.fastq", true, {0, 45, 218}};
INSTANTIATE_TEST_SUITE_P(fastq_file, sequence_file_seek_test, ::testing::Values(fastq_file_fixture));
sequence_file_seek_test_fixture sam_file_fixture{"standard.sam", true, {49, 107, 293}};
INSTANTIATE_TEST_SUITE_P(sam_file, sequence_file_seek_test, ::testing::Values(sam_file_fixture));
sequence_file_seek_test_fixture embl_file_fixture{"standard.embl", false, {0, 108, 283}};
INSTANTIATE_TEST_SUITE_P(embl_file, sequence_file_seek_test, ::testing::Values(embl_file_fixture));
sequence_file_seek_test_fixture genbank_file_fixture{"standard.genbank", false, {0, 561, 802}};
INSTANTIATE_TEST_SUITE_P(genbank_file, sequence_file_seek_test, ::testing::Values(genbank_file_fixture));
|
