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[MISC] Restructure file formats to now hold a stream handle.
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@smehringer
smehringer committed Jul 9, 2019
1 parent 7324e7b commit 50d1e48
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Showing 34 changed files with 1,254 additions and 1,064 deletions.
118 changes: 75 additions & 43 deletions include/seqan3/io/alignment_file/format_bam.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@

#include <seqan3/alphabet/detail/convert.hpp>
#include <seqan3/alphabet/nucleotide/sam_dna16.hpp>
#include <seqan3/contrib/stream/bgzf_istream.hpp>
#include <seqan3/contrib/stream/bgzf_ostream.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/char_operations/predicate.hpp>
#include <seqan3/core/concept/core_language.hpp>
Expand All @@ -37,6 +39,7 @@
#include <seqan3/io/detail/ignore_output_iterator.hpp>
#include <seqan3/io/detail/misc.hpp>
#include <seqan3/range/detail/misc.hpp>
#include <seqan3/range/view/istreambuf.hpp>
#include <seqan3/range/view/slice.hpp>
#include <seqan3/range/view/take_exactly.hpp>
#include <seqan3/range/view/take_until.hpp>
Expand Down Expand Up @@ -87,31 +90,41 @@ struct alignment_record_core
int32_t tlen; //!< The template length of the read and its mate.
};

//!\brief The seqan3::alignment_file_input_format specialisation that handles formatted BAM input.
//!\ingroup alignment_file
template <>
class alignment_file_input_format<format_bam> : alignment_file_input_format<format_sam>
/*!\brief The seqan3::alignment_file_input_format specialisation that handles formatted BAM input.
* \ingroup alignment_file
* \tparam stream_char_type The underlying character of the stream (usually `char`).
*/
template <typename stream_char_type>
class alignment_file_input_format<format_bam, stream_char_type> :
alignment_file_input_format<format_sam, stream_char_type>
{
private:
//!\brief The SAM format type that this class inherits from.
using sam_fmt = alignment_file_input_format<format_sam, stream_char_type>;

public:
//!\brief Exposes the format tag that this class is specialised with
using format_tag = format_bam;

/*!\name Constructors, destructor and assignment
* \{
*/
alignment_file_input_format() noexcept = default; //!< Defaulted.
alignment_file_input_format() = default; //!< Defaulted.
//!\brief Copy construction is explicitly deleted, because you can't have multiple access to the same file.
alignment_file_input_format(alignment_file_input_format const &) = delete;
//!\brief Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
alignment_file_input_format & operator=(alignment_file_input_format const &) = delete;
alignment_file_input_format(alignment_file_input_format &&) noexcept = default; //!< Defaulted.
alignment_file_input_format & operator=(alignment_file_input_format &&) noexcept = default; //!< Defaulted.
~alignment_file_input_format() noexcept = default; //!< Defaulted.
alignment_file_input_format(alignment_file_input_format &&) = default; //!< Defaulted.
alignment_file_input_format & operator=(alignment_file_input_format &&) = default; //!< Defaulted.
~alignment_file_input_format() = default; //!< Defaulted.

alignment_file_input_format(std::basic_istream<stream_char_type> & stream) :
stream_ptr{new contrib::basic_bgzf_istream<stream_char_type>{stream}}
{}
//!\}

//!\copydoc AlignmentFileInputFormat::read
template <typename stream_type, // constraints checked by file
typename seq_legal_alph_type,
template <typename seq_legal_alph_type,
typename ref_seqs_type,
typename ref_ids_type,
typename seq_type,
Expand All @@ -128,8 +141,7 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
typename tag_dict_type,
typename e_value_type,
typename bit_score_type>
void read(stream_type & stream,
alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
bool read(alignment_file_input_options<seq_legal_alph_type> const & SEQAN3_DOXYGEN_ONLY(options),
ref_seqs_type & ref_seqs,
alignment_file_header<ref_ids_type> & header,
seq_type & seq,
Expand Down Expand Up @@ -157,9 +169,10 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
static_assert(detail::decays_to_ignore_v<flag_type> || std::Same<flag_type, uint16_t>,
"The type of field::FLAG must be uint8_t.");

using stream_buf_t = std::istreambuf_iterator<typename stream_type::char_type>;
auto stream_view = std::ranges::subrange<decltype(stream_buf_t{stream}), decltype(stream_buf_t{})>
{stream_buf_t{stream}, stream_buf_t{}};
auto stream_view = view::istreambuf(*stream_ptr);

if (std::ranges::begin(stream_view) == std::ranges::end(stream_view)) // no records follow
return true;

// these variables need to be stored to compute the ALIGNMENT
[[maybe_unused]] int32_t offset_tmp{};
Expand All @@ -179,10 +192,10 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
read_field(stream_view, tmp32);

if (tmp32 > 0) // header text is present
read_header(stream_view | view::take_exactly_or_throw(tmp32)
| view::take_until_and_consume(is_char<'\0'>),
header,
ref_seqs);
sam_fmt::read_header(stream_view | view::take_exactly_or_throw(tmp32)
| view::take_until_and_consume(is_char<'\0'>),
header,
ref_seqs);

int32_t n_ref;
read_field(stream_view, n_ref);
Expand Down Expand Up @@ -220,8 +233,8 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form

header_was_read = true;

if (stream_buf_t{stream} == stream_buf_t{}) // no records follow
return;
if (std::ranges::begin(stream_view) == std::ranges::end(stream_view)) // no records follow
return true;
}

// read alignment record into buffer
Expand Down Expand Up @@ -419,12 +432,16 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
}

// Alignment object construction
construct_alignment(align, cigar, core.refID, ref_seqs, core.pos, ref_length); // inherited from SAM format
sam_fmt::construct_alignment(align, cigar, core.refID, ref_seqs, core.pos, ref_length);
}

return false;
}

protected:
//!\privatesection
//!\brief A pointer to the bgzf uncompressed stream.
std::unique_ptr<std::basic_istream<stream_char_type>> stream_ptr{nullptr};

//!\brief A variable that tracks whether the content of header has been read or not.
bool header_was_read{false};
Expand All @@ -433,7 +450,7 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
std::string string_buffer{};

// inherit read_field function from format_sam
using alignment_file_input_format<format_sam>::read_field;
using sam_fmt::read_field;

/*!\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.
Expand All @@ -459,7 +476,7 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
std::ranges::copy_n(std::ranges::begin(stream_view), sizeof(int32_t), reinterpret_cast<char *>(&target));
}

//!\copydoc seqan3::detail::alignment_file_input_format<format_sam>::read_sam_dict_vector
//!\copydoc seqan3::detail::alignment_file_input_format<format_sam,stream_char_type>::read_sam_dict_vector
template <typename stream_view_type, typename value_type>
void read_sam_dict_vector(seqan3::detail::sam_tag_variant & variant,
stream_view_type && stream_view,
Expand Down Expand Up @@ -643,31 +660,42 @@ class alignment_file_input_format<format_bam> : alignment_file_input_format<form
}
};

//!\brief The seqan3::alignment_file_output_format specialisation that can write formatted SAM.
//!\ingroup alignment_file
template <>
class alignment_file_output_format<format_bam> : alignment_file_output_format<format_sam>
/*!\brief The seqan3::alignment_file_output_format specialisation that can write formatted BAM.
* \ingroup alignment_file
* \tparam stream_char_type The underlying character of the stream (usually `char`).
*/
template <typename stream_char_type>
class alignment_file_output_format<format_bam, stream_char_type> :
alignment_file_output_format<format_sam, stream_char_type>
{
private:
//!\brief The SAM format type that this class inherits from.
using sam_fmt = alignment_file_output_format<format_sam, stream_char_type>;

public:
//!\brief Exposes the format tag that this class is specialised with
using format_tag = format_bam;

/*!\name Constructors, destructor and assignment
* \{
*/
alignment_file_output_format() noexcept = default; //!< Defaulted.
alignment_file_output_format() = default; //!< Defaulted.
//!\brief Copy construction is explicitly deleted, because you can't have multiple access to the same file.
alignment_file_output_format(alignment_file_output_format const &) = delete;
//!\brief Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
alignment_file_output_format & operator=(alignment_file_output_format const &) = delete;
alignment_file_output_format(alignment_file_output_format &&) noexcept = default; //!< Defaulted.
alignment_file_output_format & operator=(alignment_file_output_format &&) noexcept = default; //!< Defaulted.
~alignment_file_output_format() noexcept = default; //!< Defaulted.
alignment_file_output_format(alignment_file_output_format &&) = default; //!< Defaulted.
alignment_file_output_format & operator=(alignment_file_output_format &&) = default; //!< Defaulted.
~alignment_file_output_format() = default; //!< Defaulted.

//!\brief Construct from an output stream to write to.
alignment_file_output_format(std::basic_ostream<stream_char_type> & stream) :
stream_ptr{new contrib::basic_bgzf_ostream<stream_char_type>{stream}}
{}
//!\}

//!\copydoc AlignmentFileOutputFormat::write
template <typename stream_type,
typename header_type,
template <typename header_type,
typename seq_type,
typename id_type,
typename ref_seq_type,
Expand All @@ -676,8 +704,7 @@ class alignment_file_output_format<format_bam> : alignment_file_output_format<fo
typename qual_type,
typename mate_type,
typename tag_dict_type>
void write([[maybe_unused]] stream_type & stream,
[[maybe_unused]] alignment_file_output_options const & options,
void write([[maybe_unused]] alignment_file_output_options const & options,
[[maybe_unused]] header_type && header,
[[maybe_unused]] seq_type && seq,
[[maybe_unused]] qual_type && qual,
Expand Down Expand Up @@ -771,20 +798,21 @@ class alignment_file_output_format<format_bam> : alignment_file_output_format<fo
if (ref_offset.has_value() && (ref_offset.value() + 1) < 0)
throw format_error{detail::to_string("The ref_offset object must be >= -1 but is: ", ref_offset)};

seqan3::ostreambuf_iterator stream_it{stream};
seqan3::ostreambuf_iterator stream_it{*stream_ptr};

// ---------------------------------------------------------------------
// Writing the Header on first call
// ---------------------------------------------------------------------
if (!written_header)
if (!sam_fmt::written_header)
{
stream << "BAM\1";
std::ranges::copy(std::string_view{"BAM\1"}, stream_it);
std::ostringstream os;
write_header(os, options, header); // write header to temporary stream to query the size.
sam_fmt sf{os};
sf.write_header(options, header); // write header to temporary stream to query the size.
int32_t l_text{static_cast<int32_t>(os.str().size())};
std::ranges::copy_n(reinterpret_cast<char *>(&l_text), 4, stream_it); // write read id

stream << os.str();
std::ranges::copy(os.str(), stream_it);

int32_t n_ref{static_cast<int32_t>(header.ref_ids().size())};
std::ranges::copy_n(reinterpret_cast<char *>(&n_ref), 4, stream_it); // write read id
Expand All @@ -800,7 +828,7 @@ class alignment_file_output_format<format_bam> : alignment_file_output_format<fo
std::ranges::copy_n(reinterpret_cast<char *>(&get<0>(header.ref_id_info[ridx])), 4, stream_it);
}

written_header = true;
sam_fmt::written_header = true;
}

// ---------------------------------------------------------------------
Expand Down Expand Up @@ -959,10 +987,14 @@ class alignment_file_output_format<format_bam> : alignment_file_output_format<fo
}

// write optional fields
stream << tag_dict_binary_str;
std::ranges::copy_n(tag_dict_binary_str.begin(), tag_dict_binary_str.size(), stream_it);
} // if constexpr (!detail::decays_to_ignore_v<header_type>)
}

private:
//!\brief A pointer to the bgzf uncompressed stream.
std::unique_ptr<std::basic_ostream<stream_char_type>> stream_ptr{nullptr};

//!\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
{
Expand Down
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