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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 <gtest/gtest.h>
#include <seqan3/std/iterator>
#include <string>
#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/detail/to_string.hpp>
#include <seqan3/core/detail/debug_stream_alphabet.hpp>
#include <seqan3/core/detail/debug_stream_range.hpp>
#include <seqan3/io/alignment_file/detail.hpp>
#include <seqan3/test/expect_range_eq.hpp>
using seqan3::operator""_dna4;
template <typename t>
class aligned_sequence : public ::testing::Test
{};
seqan3::dna4_vector const seq = "ACTA"_dna4;
TYPED_TEST_SUITE_P(aligned_sequence);
TYPED_TEST_P(aligned_sequence, fulfills_concept)
{
EXPECT_TRUE((seqan3::aligned_sequence<TypeParam>));
EXPECT_FALSE((seqan3::aligned_sequence<std::vector<seqan3::dna4>>));
}
TYPED_TEST_P(aligned_sequence, assign_unaligned_sequence)
{
using unaligned_seq_type = std::remove_cvref_t<seqan3::detail::unaligned_seq_t<TypeParam>>;
unaligned_seq_type unaligned_seq{};
if constexpr (seqan3::sequence_container<unaligned_seq_type>)
{
unaligned_seq.resize(seq.size());
std::copy(seq.begin(), seq.end(), std::ranges::begin(unaligned_seq));
}
else // type is view, happens for gap_decorator tests
unaligned_seq = unaligned_seq_type{seq};
TypeParam aligned_seq{};
assign_unaligned(aligned_seq, unaligned_seq);
EXPECT_EQ(aligned_seq.size(), unaligned_seq.size());
EXPECT_RANGE_EQ(aligned_seq, unaligned_seq);
}
TYPED_TEST_P(aligned_sequence, assign_empty_unaligned_sequence)
{
using unaligned_seq_type = std::remove_cvref_t<seqan3::detail::unaligned_seq_t<TypeParam>>;
unaligned_seq_type unaligned_seq{};
TypeParam aligned_seq{};
assign_unaligned(aligned_seq, unaligned_seq);
EXPECT_EQ(aligned_seq.size(), unaligned_seq.size());
EXPECT_EQ(aligned_seq.size(), 0u);
}
TYPED_TEST_P(aligned_sequence, insert_one_gap)
{
TypeParam aligned_seq;
TestFixture::initialise_typed_test_container(aligned_seq, seq);
EXPECT_EQ(aligned_seq.size(), 4u);
auto it = seqan3::insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 1));
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(aligned_seq[1], seqan3::gap{});
EXPECT_EQ(aligned_seq.size(), 5u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A-CTA");
it = seqan3::insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 1));
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(aligned_seq[1], seqan3::gap{});
EXPECT_EQ(aligned_seq[2], seqan3::gap{});
EXPECT_EQ(aligned_seq.size(), 6u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A--CTA");
}
TYPED_TEST_P(aligned_sequence, insert_multiple_gaps)
{
TypeParam aligned_seq;
TestFixture::initialise_typed_test_container(aligned_seq, seq);
EXPECT_EQ(aligned_seq.size(), 4u);
auto it = seqan3::insert_gap(aligned_seq, std::ranges::next(begin(aligned_seq), 1), 2);
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(*++it, seqan3::gap{});
EXPECT_EQ(aligned_seq[1], seqan3::gap{});
EXPECT_EQ(aligned_seq[2], seqan3::gap{});
EXPECT_EQ(aligned_seq.size(), 6u);
// insert a gap within another gap
seqan3::insert_gap(aligned_seq, std::ranges::next(begin(aligned_seq), 2), 4);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A------CTA");
// insert at begin
seqan3::insert_gap(aligned_seq, std::ranges::begin(aligned_seq), 2);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "--A------CTA");
// insert at end
seqan3::insert_gap(aligned_seq, std::ranges::end(aligned_seq), 2);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "--A------CTA--");
}
TYPED_TEST_P(aligned_sequence, insert_zero_gaps)
{
TypeParam aligned_seq;
TestFixture::initialise_typed_test_container(aligned_seq, seq);
EXPECT_EQ(aligned_seq.size(), 4u);
auto it = seqan3::insert_gap(aligned_seq, std::ranges::next(begin(aligned_seq), 1), 0);
typename TypeParam::value_type val{'C'_dna4};
EXPECT_EQ(*it, val);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
}
TYPED_TEST_P(aligned_sequence, erase_one_gap)
{
// 1) Removing an actual gap
TypeParam aligned_seq;
TestFixture::initialise_typed_test_container(aligned_seq, seq);
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
insert_gap(aligned_seq, std::ranges::next(begin(aligned_seq), 1));
EXPECT_EQ(aligned_seq.size(), 5u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A-CTA");
typename TypeParam::value_type val{'C'_dna4};
auto it = seqan3::erase_gap(aligned_seq, std::ranges::next(begin(aligned_seq), 1));
EXPECT_EQ(*it, val);
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
// 2) Removing a non-gap
EXPECT_THROW(seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 2)),
seqan3::gap_erase_failure);
EXPECT_EQ(aligned_seq.size(), 4u); // no change
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
}
TYPED_TEST_P(aligned_sequence, erase_multiple_gaps)
{
TypeParam aligned_seq;
// 1) Removing a gap of length > 1
TestFixture::initialise_typed_test_container(aligned_seq, seq);
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
seqan3::insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 1), 2);
EXPECT_EQ(aligned_seq.size(), 6u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A--CTA");
typename TypeParam::value_type val{'C'_dna4};
auto it = seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 1),
std::ranges::next(std::ranges::begin(aligned_seq), 3));
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(*it, val);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
// 2) Removing a non-gap
TestFixture::initialise_typed_test_container(aligned_seq, seq); // reset
EXPECT_THROW(seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 1),
std::ranges::next(std::ranges::begin(aligned_seq), 3)),
seqan3::gap_erase_failure);
EXPECT_EQ(aligned_seq.size(), seq.size()); // no change
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "ACTA");
// 3) Remove a gap of length 1 within a gap of length 5
TestFixture::initialise_typed_test_container(aligned_seq, seq); // reset
insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 1), 5);
EXPECT_EQ(aligned_seq.size(), seq.size() + 5);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A-----CTA");
it = erase_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 3)); // erase one in the middle of 5
EXPECT_EQ(aligned_seq.size(), seq.size() + 4);
EXPECT_EQ(aligned_seq[5], val);
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A----CTA");
// 4) Remove gaps two times
TestFixture::initialise_typed_test_container(aligned_seq, seq); // reset
insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 3), 4);
insert_gap(aligned_seq, std::ranges::next(std::ranges::begin(aligned_seq), 1), 5);
EXPECT_EQ(aligned_seq.size(), seq.size() + 9);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A-----CT----A");
seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 2),
std::ranges::next(std::ranges::begin(aligned_seq), 4));
seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 6),
std::ranges::next(std::ranges::begin(aligned_seq), 10));
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A---CTA");
// 5) Removing too much from a gap
EXPECT_THROW(seqan3::erase_gap(aligned_seq,
std::ranges::next(std::ranges::begin(aligned_seq), 2),
std::ranges::next(std::ranges::begin(aligned_seq), 5)),
seqan3::gap_erase_failure);
EXPECT_EQ(aligned_seq.size(), 7u); // no change
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "A---CTA");
}
TYPED_TEST_P(aligned_sequence, insert_erase_on_empty_sequence)
{
using unaligned_seq_type = std::remove_cvref_t<seqan3::detail::unaligned_seq_t<TypeParam>>;
unaligned_seq_type unaligned{};
TypeParam aligned_seq{};
assign_unaligned(aligned_seq, unaligned);
auto it = insert_gap(aligned_seq, std::ranges::begin(aligned_seq));
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(aligned_seq.size(), 1u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "-");
it = seqan3::insert_gap(aligned_seq, std::ranges::end(aligned_seq), 3);
EXPECT_EQ(*it, seqan3::gap{});
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "----");
it = seqan3::insert_gap(aligned_seq, std::ranges::end(aligned_seq), 0);
EXPECT_EQ(aligned_seq.size(), 4u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "----");
it = seqan3::erase_gap(aligned_seq, std::ranges::begin(aligned_seq));
EXPECT_EQ(aligned_seq.size(), 3u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "---");
it = seqan3::erase_gap(aligned_seq, std::ranges::begin(aligned_seq), std::ranges::end(aligned_seq));
EXPECT_EQ(aligned_seq.size(), 0u);
EXPECT_EQ(seqan3::detail::to_string(aligned_seq), "");
}
TYPED_TEST_P(aligned_sequence, cigar_string)
{
{ // default_parameters
auto seq_ref = "ACGTGATCTG"_dna4;
auto seq_read = "ACGTCGTAGTG"_dna4;
TypeParam ref;
TypeParam read;
TestFixture::initialise_typed_test_container(ref, seq_ref);
TestFixture::initialise_typed_test_container(read, seq_read);
seqan3::insert_gap(ref, std::ranges::next(begin(ref), 7), 2);
seqan3::insert_gap(read, std::ranges::next(begin(read), 4), 1);
std::string expected = "4M1D2M2I3M";
EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read)));
TypeParam ref2;
TypeParam read2;
TestFixture::initialise_typed_test_container(ref2, seq_ref);
TestFixture::initialise_typed_test_container(read2, seq_read);
insert_gap(ref2, std::ranges::next(begin(ref2), 10), 2);
insert_gap(ref2, std::ranges::next(begin(ref2), 7), 2);
insert_gap(ref2, std::ranges::begin(ref2), 3);
insert_gap(read2, std::ranges::next(begin(read2), 11), 4);
insert_gap(read2, std::ranges::next(begin(read2), 4), 1);
insert_gap(read2, std::ranges::begin(read2), 1);
std::string expected2 = "1P2I2M1D4M2I1M2D2P";
EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2)));
}
{
// with soft clipping
auto seq_ref = "ACGTGATCTG"_dna4;
auto seq_read = "ACGTCGTAGTG"_dna4;
TypeParam ref;
TypeParam read;
TestFixture::initialise_typed_test_container(ref, seq_ref);
TestFixture::initialise_typed_test_container(read, seq_read);
insert_gap(ref, std::ranges::next(std::ranges::begin(ref), 7), 2);
insert_gap(read, std::ranges::next(std::ranges::begin(read), 4), 1);
std::string expected = "5S4M1D2M2I3M60S";
EXPECT_EQ(expected, seqan3::detail::get_cigar_string(std::make_pair(ref, read), 5, 60));
// gaps at the end
TypeParam ref2;
TypeParam read2;
TestFixture::initialise_typed_test_container(ref2, seq_ref);
TestFixture::initialise_typed_test_container(read2, seq_read);
seqan3::insert_gap(ref2, std::ranges::next(begin(ref2), 10), 2);
seqan3::insert_gap(ref2, std::ranges::next(begin(ref2), 7), 2);
seqan3::insert_gap(ref2, std::ranges::begin(ref2), 3);
seqan3::insert_gap(read2, std::ranges::next(begin(read2), 11), 4);
seqan3::insert_gap(read2, std::ranges::next(begin(read2), 4), 1);
seqan3::insert_gap(read2, std::ranges::begin(read2), 1);
std::string expected2 = "3S1P2I2M1D4M2I1M2D2P5S";
EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref2, read2), 3, 5));
}
{
// no gaps at the end
auto seq_ref = "ACGTGATCAG"_dna4;
auto seq_read = "ACGTCGTACTG"_dna4;
TypeParam ref;
TypeParam read;
TestFixture::initialise_typed_test_container(ref, seq_ref);
TestFixture::initialise_typed_test_container(read, seq_read);
seqan3::insert_gap(ref, std::ranges::next(std::ranges::begin(ref), 7), 2);
seqan3::insert_gap(read, std::ranges::next(std::ranges::begin(read), 4), 1);
std::string expected1 = "4=1D2X2I1=1X1=";
std::string expected2 = "5S4=1D2X2I1=1X1=60S";
EXPECT_EQ(expected1, seqan3::detail::get_cigar_string(std::make_pair(ref, read), 0, 0, true));
EXPECT_EQ(expected2, seqan3::detail::get_cigar_string(std::make_pair(ref, read), 5, 60, true));
}
}
REGISTER_TYPED_TEST_SUITE_P(aligned_sequence,
fulfills_concept,
assign_unaligned_sequence,
assign_empty_unaligned_sequence,
insert_erase_on_empty_sequence,
insert_one_gap,
insert_multiple_gaps,
insert_zero_gaps,
erase_one_gap,
erase_multiple_gaps,
cigar_string);
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