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
|
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <seqan3/std/algorithm>
#include <sstream>
#include <gtest/gtest.h>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/core/concept/tuple.hpp>
#include <seqan3/io/detail/record.hpp>
#include <seqan3/io/record.hpp>
#include <seqan3/test/expect_range_eq.hpp>
using seqan3::operator""_dna4;
using default_fields = seqan3::fields<seqan3::field::seq, seqan3::field::id, seqan3::field::qual>;
// This is needed for EXPECT_RANGE_EQ:
namespace seqan3
{
template <typename char_t>
inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, field f)
{
stream << "<field: " << static_cast<size_t>(f) << ">";
return stream;
}
} // namespace seqan3
// ----------------------------------------------------------------------------
// fields
// ----------------------------------------------------------------------------
TEST(fields, usage)
{
std::array comp{seqan3::field::seq, seqan3::field::id, seqan3::field::qual};
EXPECT_RANGE_EQ(default_fields::as_array, comp);
EXPECT_TRUE(default_fields::contains(seqan3::field::seq));
EXPECT_TRUE(default_fields::contains(seqan3::field::id));
EXPECT_TRUE(default_fields::contains(seqan3::field::qual));
EXPECT_FALSE(default_fields::contains(seqan3::field::seq_qual));
EXPECT_EQ(default_fields::index_of(seqan3::field::seq), 0ul);
EXPECT_EQ(default_fields::index_of(seqan3::field::id), 1ul);
EXPECT_EQ(default_fields::index_of(seqan3::field::qual), 2ul);
}
// ----------------------------------------------------------------------------
// record
// ----------------------------------------------------------------------------
struct record : public ::testing::Test
{
using types = seqan3::type_list<std::string, seqan3::dna4_vector>;
using types_as_ids = seqan3::fields<seqan3::field::id, seqan3::field::seq>;
using record_type = seqan3::record<types, types_as_ids>;
};
TEST_F(record, definition_tuple_traits)
{
EXPECT_TRUE((std::is_same_v<typename record_type::base_type,
std::tuple<std::string, seqan3::dna4_vector>>));
EXPECT_TRUE((std::is_same_v<std::tuple_element_t<0, record_type>,
std::string>));
EXPECT_TRUE((std::is_same_v<std::tuple_element_t<1, record_type>,
seqan3::dna4_vector>));
EXPECT_EQ(std::tuple_size_v<record_type>, 2ul);
EXPECT_TRUE(seqan3::tuple_like<record_type>);
}
TEST_F(record, construction)
{
[[maybe_unused]] record_type r{"MY ID", "ACGT"_dna4};
}
TEST_F(record, get_by_index)
{
record_type r{"MY ID", "ACGT"_dna4};
EXPECT_EQ(std::get<0>(r), "MY ID");
EXPECT_RANGE_EQ(std::get<1>(r), "ACGT"_dna4);
}
TEST_F(record, get_by_type)
{
record_type r{"MY ID", "ACGT"_dna4};
EXPECT_EQ(std::get<std::string>(r), "MY ID");
EXPECT_RANGE_EQ(std::get<seqan3::dna4_vector>(r), "ACGT"_dna4);
}
TEST_F(record, get_by_field)
{
record_type r{"MY ID", "ACGT"_dna4};
EXPECT_EQ(seqan3::get<seqan3::field::id>(r), "MY ID");
EXPECT_RANGE_EQ(seqan3::get<seqan3::field::seq>(r), "ACGT"_dna4);
}
// ----------------------------------------------------------------------------
// detail/record.hpp
// ----------------------------------------------------------------------------
TEST(detail, select_types_with_ids)
{
using types = seqan3::type_list<std::string, seqan3::dna4_vector, std::vector<seqan3::phred42>>;
using types_as_ids = seqan3::fields<seqan3::field::id, seqan3::field::seq, seqan3::field::qual>;
using selected_ids = seqan3::fields<seqan3::field::qual, seqan3::field::id>;
using selected_types = typename seqan3::detail::select_types_with_ids<types, types_as_ids, selected_ids>::type;
EXPECT_TRUE((std::is_same_v<selected_types, seqan3::type_list<std::vector<seqan3::phred42>, std::string>>));
}
|
