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// -----------------------------------------------------------------------------------------------------
// 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 <sstream>
#include <string>
#include <vector>
#include <gtest/gtest.h>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/all.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/test/pretty_printing.hpp>
#include "sequence_file_format_test_template.hpp"
template <>
struct sequence_file_read<seqan3::format_sam> : public sequence_file_data
{
std::string standard_input
{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++-
ID2 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE
ID3 lala 0 * 0 0 * * 0 0 ACGTTTA !!!!!!!
)"
};
std::string illegal_alphabet_character_input
{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTT?TTTTTTT !##$%&'()*+,-./++-
)"
};
std::string standard_output
{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++-
ID2 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE
ID3 lala 0 * 0 0 * * 0 0 ACGTTTA !!!!!!!
)"
};
std::string no_or_ill_formatted_id_input
{
R"(* 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++-
)"
};
};
// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------
INSTANTIATE_TYPED_TEST_SUITE_P(sam, sequence_file_read, seqan3::format_sam, );
INSTANTIATE_TYPED_TEST_SUITE_P(sam, sequence_file_write, seqan3::format_sam, );
// ----------------------------------------------------------------------------
// reading
// ----------------------------------------------------------------------------
struct read_sam : sequence_file_read<seqan3::format_sam>
{
seqan3::sequence_file_input_options<seqan3::dna5, false> options{};
void do_read_test(std::string const & input)
{
std::stringstream istream{input};
seqan3::sequence_file_input fin{istream, seqan3::format_sam{}};
auto it = fin.begin();
for (unsigned i = 0; i < 3; ++i, it++)
{
EXPECT_EQ(seqan3::get<seqan3::field::seq>(*it), seqs[i]);
EXPECT_EQ(seqan3::get<seqan3::field::id>(*it), ids[i]);
EXPECT_EQ(seqan3::get<seqan3::field::qual>(*it), quals[i]);
}
}
};
TEST_F(read_sam, tags)
{
std::string input
{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++- FI:i:1
ID2 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE AS:i:3
ID3 lala 0 * 0 0 * * 0 0 ACGTTTA !!!!!!! TI:i:2
)"
};
do_read_test(input);
}
TEST_F(read_sam, mixed_issues)
{
std::string input
{
R"(ID1 0 BABABA 200 0 * BABABA 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++- FI:i:1
ID2 0 * 0 0 BABA * 30 0 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE
ID3 lala 0 * 0 0 HAHAHAHA+ * 0 0 ACGTTTA !!!!!!!
)"
};
do_read_test(input);
}
TEST_F(read_sam, no_qual)
{
std::string input
{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT *
ID2 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDE
ID3 lala 0 * 0 0 * * 0 0 ACGTTTA !!!!!!!
)"
};
quals[0] = { ""_phred42 };
do_read_test(input);
}
TEST_F(read_sam, qual_too_short)
{
std::stringstream istream{std::string{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()-./++-
)"}};
seqan3::sequence_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
TEST_F(read_sam, qual_too_long)
{
std::stringstream istream{std::string{
R"(ID1 0 * 0 0 * * 0 0 ACGTTTTTTTTTTTTTTT !##$%&'()*+,-./++-+
)"}};
seqan3::sequence_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
TEST_F(read_sam, no_seq)
{
std::stringstream istream{std::string{
R"(ID 1 0 * 0 0 * * 0 0 * !##$%&'()*+,-./++-
)"}};
seqan3::sequence_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}
// ----------------------------------------------------------------------------
// writing
// ----------------------------------------------------------------------------
struct write : public ::testing::Test
{
std::vector<seqan3::dna5_vector> seqs
{
"ACGT"_dna5,
"AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN"_dna5,
"GGAGTATAATATATATATATAT"_dna5
};
std::vector<std::string> ids
{
"TEST 1",
"Test2",
"Test3"
};
std::vector<std::vector<seqan3::phred42>> quals
{
{ "!##$"_phred42 },
{ "!##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE"_phred42 },
{ "!!*+,-./+*+,-./+!!FF!!"_phred42 },
};
seqan3::sequence_file_output_options options{};
std::ostringstream ostream;
void do_write_test()
{
seqan3::sequence_file_output fout{ostream, seqan3::format_sam{}};
for (unsigned i = 0; i < 3; ++i)
EXPECT_NO_THROW(( fout.emplace_back(seqs[i], ids[i], quals[i]) ));
ostream.flush();
}
void do_write_test_no_qual()
{
seqan3::sequence_file_output fout{ostream, seqan3::format_sam{}};
for (unsigned i = 0; i < 3; ++i)
EXPECT_NO_THROW(( fout.emplace_back(seqs[i], ids[i], ""_phred42) ));
ostream.flush();
}
};
TEST_F(write, no_id)
{
std::string comp
{
R"(* 0 * 0 0 * * 0 0 ACGT !##$
Test2 0 * 0 0 * * 0 0 AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN !##$&'()*+,-./+)*+,-)*+,-)*+,-)*+,BDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDEBDBDDEBDBEEBEBE
Test3 0 * 0 0 * * 0 0 GGAGTATAATATATATATATAT !!*+,-./+*+,-./+!!FF!!
)"
};
ids[0] = "";
do_write_test();
EXPECT_EQ(ostream.str(), comp);
}
TEST_F(write, no_seq)
{
std::string comp
{
R"(TEST 1 0 * 0 0 * * 0 0 * *
Test2 0 * 0 0 * * 0 0 AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN *
Test3 0 * 0 0 * * 0 0 GGAGTATAATATATATATATAT *
)"
};
seqs[0] = ""_dna5;
do_write_test_no_qual();
EXPECT_EQ(ostream.str(), comp);
}
// No qualities given
TEST_F(write, no_qual)
{
std::string comp
{
R"(TEST 1 0 * 0 0 * * 0 0 ACGT *
Test2 0 * 0 0 * * 0 0 AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN *
Test3 0 * 0 0 * * 0 0 GGAGTATAATATATATATATAT *
)"
};
do_write_test_no_qual();
EXPECT_EQ(ostream.str(), comp);
}
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