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[MISC] clang-format
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seqan-actions committed Oct 4, 2022
1 parent d17fd02 commit dc407de
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Showing 4 changed files with 63 additions and 64 deletions.
116 changes: 58 additions & 58 deletions include/seqan3/io/sam_file/format_bam.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -158,78 +158,78 @@ class format_bam : private detail::format_sam_base
};

//!\brief Converts a cigar op character to the rank according to the official BAM specifications.
static constexpr std::array<uint8_t, 256> char_to_sam_rank{[]() constexpr {std::array<uint8_t, 256> ret{};

using index_t = std::make_unsigned_t<char>;

// ret['M'] = 0; set anyway by initialization
ret[static_cast<index_t>('I')] = 1;
ret[static_cast<index_t>('D')] = 2;
ret[static_cast<index_t>('N')] = 3;
ret[static_cast<index_t>('S')] = 4;
ret[static_cast<index_t>('H')] = 5;
ret[static_cast<index_t>('P')] = 6;
ret[static_cast<index_t>('=')] = 7;
ret[static_cast<index_t>('X')] = 8;

return ret;
}()
}; // namespace seqan3

//!\brief Computes the bin number for a given region [beg, end), copied from the official SAM specifications.
static uint16_t reg2bin(int32_t beg, int32_t end) noexcept
{
--end;
if (beg >> 14 == end >> 14)
return ((1 << 15) - 1) / 7 + (beg >> 14);
if (beg >> 17 == end >> 17)
return ((1 << 12) - 1) / 7 + (beg >> 17);
if (beg >> 20 == end >> 20)
return ((1 << 9) - 1) / 7 + (beg >> 20);
if (beg >> 23 == end >> 23)
return ((1 << 6) - 1) / 7 + (beg >> 23);
if (beg >> 26 == end >> 26)
return ((1 << 3) - 1) / 7 + (beg >> 26);
return 0;
}
static constexpr std::array<uint8_t, 256> char_to_sam_rank{[]() constexpr
{
std::array<uint8_t, 256> ret{};

using index_t = std::make_unsigned_t<char>;

// ret['M'] = 0; set anyway by initialization
ret[static_cast<index_t>('I')] = 1;
ret[static_cast<index_t>('D')] = 2;
ret[static_cast<index_t>('N')] = 3;
ret[static_cast<index_t>('S')] = 4;
ret[static_cast<index_t>('H')] = 5;
ret[static_cast<index_t>('P')] = 6;
ret[static_cast<index_t>('=')] = 7;
ret[static_cast<index_t>('X')] = 8;

return ret;
}()}; // namespace seqan3

//!\brief Computes the bin number for a given region [beg, end), copied from the official SAM specifications.
static uint16_t reg2bin(int32_t beg, int32_t end) noexcept
{
--end;
if (beg >> 14 == end >> 14)
return ((1 << 15) - 1) / 7 + (beg >> 14);
if (beg >> 17 == end >> 17)
return ((1 << 12) - 1) / 7 + (beg >> 17);
if (beg >> 20 == end >> 20)
return ((1 << 9) - 1) / 7 + (beg >> 20);
if (beg >> 23 == end >> 23)
return ((1 << 6) - 1) / 7 + (beg >> 23);
if (beg >> 26 == end >> 26)
return ((1 << 3) - 1) / 7 + (beg >> 26);
return 0;
}

/*!\brief Reads a arithmetic field from binary stream by directly reinterpreting the bits.
/*!\brief Reads a arithmetic field from binary stream by directly reinterpreting the bits.
* \tparam stream_view_type The type of the stream as a view.
* \tparam number_type The type of number to parse; must model std::integral.
* \param[in, out] stream_view The stream view to read from.
* \param[out] target An integral value to store the parsed value in.
*/
template <typename stream_view_type, std::integral number_type>
void read_integral_byte_field(stream_view_type && stream_view, number_type & target)
{
std::ranges::copy_n(std::ranges::begin(stream_view), sizeof(target), reinterpret_cast<char *>(&target));
}
template <typename stream_view_type, std::integral number_type>
void read_integral_byte_field(stream_view_type && stream_view, number_type & target)
{
std::ranges::copy_n(std::ranges::begin(stream_view), sizeof(target), reinterpret_cast<char *>(&target));
}

/*!\brief Reads a float field from binary stream by directly reinterpreting the bits.
/*!\brief Reads a float field from binary stream by directly reinterpreting the bits.
* \tparam stream_view_type The type of the stream as a view.
* \param[in, out] stream_view The stream view to read from.
* \param[out] target An float value to store the parsed value in.
*/
template <typename stream_view_type>
void read_float_byte_field(stream_view_type && stream_view, float & target)
{
std::ranges::copy_n(std::ranges::begin(stream_view), sizeof(int32_t), reinterpret_cast<char *>(&target));
}
template <typename stream_view_type>
void read_float_byte_field(stream_view_type && stream_view, float & target)
{
std::ranges::copy_n(std::ranges::begin(stream_view), sizeof(int32_t), reinterpret_cast<char *>(&target));
}

template <typename stream_view_type, typename value_type>
void read_sam_dict_vector(seqan3::detail::sam_tag_variant & variant,
stream_view_type && stream_view,
value_type const & SEQAN3_DOXYGEN_ONLY(value));
template <typename stream_view_type, typename value_type>
void read_sam_dict_vector(seqan3::detail::sam_tag_variant & variant,
stream_view_type && stream_view,
value_type const & SEQAN3_DOXYGEN_ONLY(value));

template <typename stream_view_type>
void read_sam_dict_field(stream_view_type && stream_view, sam_tag_dictionary & target);
template <typename stream_view_type>
void read_sam_dict_field(stream_view_type && stream_view, sam_tag_dictionary & target);

template <typename cigar_input_type>
auto parse_binary_cigar(cigar_input_type && cigar_input, uint16_t n_cigar_op) const;
template <typename cigar_input_type>
auto parse_binary_cigar(cigar_input_type && cigar_input, uint16_t n_cigar_op) const;

static std::string get_tag_dict_str(sam_tag_dictionary const & tag_dict);
}
;
static std::string get_tag_dict_str(sam_tag_dictionary const & tag_dict);
};

//!\copydoc sam_file_input_format::read_alignment_record
template <typename stream_type, // constraints checked by file
Expand Down Expand Up @@ -284,7 +284,7 @@ format_bam::read_alignment_record(stream_type & stream,

auto stream_view = seqan3::detail::istreambuf(stream);

[[maybe_unused]] int32_t offset_tmp{}; // needed in case the cigar string was stored in the tag dictionary
[[maybe_unused]] int32_t offset_tmp{}; // needed in case the cigar string was stored in the tag dictionary
[[maybe_unused]] int32_t ref_length{0}; // needed in case the cigar string was stored in the tag dictionary

// Header
Expand Down
3 changes: 2 additions & 1 deletion include/seqan3/io/sam_file/input.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -369,7 +369,8 @@ class sam_file_input
field::header_ptr>;

static_assert(
[]() constexpr {
[]() constexpr
{
for (field f : selected_field_ids::as_array)
if (!field_ids::contains(f))
return false;
Expand Down
3 changes: 2 additions & 1 deletion include/seqan3/io/sam_file/output.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,8 @@ class sam_file_output
field::header_ptr>;

static_assert(
[]() constexpr {
[]() constexpr
{
for (field f : selected_field_ids::as_array)
if (!field_ids::contains(f))
return false;
Expand Down
5 changes: 1 addition & 4 deletions test/unit/io/sam_file/format_bam_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,6 @@ TEST_F(bam_format, too_long_cigar_string_write)
}
too_long_cigar.push_back({1, 'M'_cigar_operation});


// Expected output. ATTENTION this could not be validated by samtools as it does not support too long cigar strings
std::string expected =
std::string /*the beginning*/
Expand Down Expand Up @@ -658,9 +657,7 @@ TEST_F(bam_format, issue2417)

std::istringstream stream{input};

seqan3::sam_file_input fin{stream,
seqan3::format_bam{},
seqan3::fields<seqan3::field::id, seqan3::field::cigar>{}};
seqan3::sam_file_input fin{stream, seqan3::format_bam{}, seqan3::fields<seqan3::field::id, seqan3::field::cigar>{}};

std::vector<seqan3::gapped<seqan3::dna5>> const empty_sequence{};

Expand Down

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