bgzf_stream_util.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2023, 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
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <algorithm>
#include <array>
#include <cassert>
#include <cstring>
#include <memory>
#include <span>
#include <thread>
 
#include <seqan3/contrib/stream/bgzf.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/io/detail/magic_header.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/utility/detail/to_little_endian.hpp>
 
#if !defined(SEQAN3_HAS_ZLIB) && !defined(SEQAN3_HEADER_TEST)
#    error "This file cannot be used when building without GZip-support."
#endif // !defined(SEQAN3_HAS_ZLIB) && !defined(SEQAN3_HEADER_TEST)
 
#if defined(SEQAN3_HAS_ZLIB)
// Zlib headers
#    include <zlib.h>
 
namespace seqan3::contrib
{
 
// ============================================================================
// Forwards
// ============================================================================
 
// ============================================================================
// Classes
// ============================================================================
 
// Special end-of-file marker defined by the BGZF compression format.
// See: https://samtools.github.io/hts-specs/SAMv1.pdf
static constexpr std::array<char, 28> BGZF_END_OF_FILE_MARKER{
    {'\x1f', '\x8b', '\x08', '\x04', '\x00', '\x00', '\x00', '\x00', '\x00', '\xff', '\x06', '\x00', '\x42', '\x43',
     '\x02', '\x00', '\x1b', '\x00', '\x03', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00', '\x00'}};
 
template <typename TAlgTag>
struct CompressionContext
{};
 
template <typename TAlgTag>
struct DefaultPageSize;
 
template <>
struct CompressionContext<detail::gz_compression>
{
    z_stream strm;
 
    CompressionContext()
    {
        std::memset(&strm, 0, sizeof(z_stream));
    }
};
 
template <>
struct CompressionContext<detail::bgzf_compression> : CompressionContext<detail::gz_compression>
{
    static constexpr size_t BLOCK_HEADER_LENGTH = detail::bgzf_compression::magic_header.size();
    unsigned char headerPos;
};
 
template <>
struct DefaultPageSize<detail::bgzf_compression>
{
    static unsigned const MAX_BLOCK_SIZE = 64 * 1024;
    static unsigned const BLOCK_FOOTER_LENGTH = 8;
    // 5 bytes block overhead (see 3.2.4. at https://tools.ietf.org/html/rfc1951)
    static unsigned const ZLIB_BLOCK_OVERHEAD = 5;
 
    // Reduce the maximal input size, such that the compressed data
    // always fits in one block even for level Z_NO_COMPRESSION.
    enum
    {
        BLOCK_HEADER_LENGTH = CompressionContext<detail::bgzf_compression>::BLOCK_HEADER_LENGTH
    };
    static unsigned const VALUE = MAX_BLOCK_SIZE - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH - ZLIB_BLOCK_OVERHEAD;
};
 
// ============================================================================
// Functions
// ============================================================================
 
// ----------------------------------------------------------------------------
// Function compressInit()
// ----------------------------------------------------------------------------
 
inline void compressInit(CompressionContext<detail::gz_compression> & ctx)
{
    int const GZIP_WINDOW_BITS = -15; // no zlib header
    int const Z_DEFAULT_MEM_LEVEL = 8;
 
    ctx.strm.zalloc = NULL;
    ctx.strm.zfree = NULL;
 
    // (weese:) We use Z_BEST_SPEED instead of Z_DEFAULT_COMPRESSION as it turned out
    //          to be 2x faster and produces only 7% bigger output
    //    int status = deflateInit2(&ctx.strm, Z_DEFAULT_COMPRESSION, Z_DEFLATED,
    //                              GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
    int status =
        deflateInit2(&ctx.strm, Z_BEST_SPEED, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
    if (status != Z_OK)
        throw io_error("Calling deflateInit2() failed for gz file.");
}
 
// ----------------------------------------------------------------------------
// Function compressInit()
// ----------------------------------------------------------------------------
 
inline void compressInit(CompressionContext<detail::bgzf_compression> & ctx)
{
    compressInit(static_cast<CompressionContext<detail::gz_compression> &>(ctx));
    ctx.headerPos = 0;
}
 
// ----------------------------------------------------------------------------
// Helper Function _bgzfUnpackXX()
// ----------------------------------------------------------------------------
 
inline uint16_t _bgzfUnpack16(char const * buffer)
{
    uint16_t tmp;
    std::uninitialized_copy(buffer, buffer + sizeof(uint16_t), reinterpret_cast<char *>(&tmp));
    return detail::to_little_endian(tmp);
}
 
inline uint32_t _bgzfUnpack32(char const * buffer)
{
    uint32_t tmp;
    std::uninitialized_copy(buffer, buffer + sizeof(uint32_t), reinterpret_cast<char *>(&tmp));
    return detail::to_little_endian(tmp);
}
 
// ----------------------------------------------------------------------------
// Helper Function _bgzfPackXX()
// ----------------------------------------------------------------------------
 
inline void _bgzfPack16(char * buffer, uint16_t value)
{
    value = detail::to_little_endian(value);
    std::uninitialized_copy(reinterpret_cast<char *>(&value),
                            reinterpret_cast<char *>(&value) + sizeof(uint16_t),
                            buffer);
}
 
inline void _bgzfPack32(char * buffer, uint32_t value)
{
    value = detail::to_little_endian(value);
    std::uninitialized_copy(reinterpret_cast<char *>(&value),
                            reinterpret_cast<char *>(&value) + sizeof(uint32_t),
                            buffer);
}
 
// ----------------------------------------------------------------------------
// Function _compressBlock()
// ----------------------------------------------------------------------------
 
template <typename TDestValue, typename TDestCapacity, typename TSourceValue, typename TSourceLength>
inline TDestCapacity _compressBlock(TDestValue * dstBegin,
                                    TDestCapacity dstCapacity,
                                    TSourceValue * srcBegin,
                                    TSourceLength srcLength,
                                    CompressionContext<detail::bgzf_compression> & ctx)
{
    const size_t BLOCK_HEADER_LENGTH = DefaultPageSize<detail::bgzf_compression>::BLOCK_HEADER_LENGTH;
    const size_t BLOCK_FOOTER_LENGTH = DefaultPageSize<detail::bgzf_compression>::BLOCK_FOOTER_LENGTH;
 
    assert(dstCapacity > BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH);
    assert(sizeof(TDestValue) == 1u);
    assert(sizeof(unsigned) == 4u);
 
    // 1. COPY HEADER
    std::ranges::copy(detail::bgzf_compression::magic_header, dstBegin);
 
    // 2. COMPRESS
    compressInit(ctx);
    ctx.strm.next_in = (Bytef *)(srcBegin);
    ctx.strm.next_out = (Bytef *)(dstBegin + BLOCK_HEADER_LENGTH);
    ctx.strm.avail_in = srcLength * sizeof(TSourceValue);
    ctx.strm.avail_out = dstCapacity - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
 
    int status = deflate(&ctx.strm, Z_FINISH);
    if (status != Z_STREAM_END)
    {
        deflateEnd(&ctx.strm);
        throw io_error("Deflation failed. Compressed BGZF data is too big.");
    }
 
    status = deflateEnd(&ctx.strm);
    if (status != Z_OK)
        throw io_error("BGZF deflateEnd() failed.");
 
    // 3. APPEND FOOTER
 
    // Set compressed length into buffer, compute CRC and write CRC into buffer.
 
    size_t len = dstCapacity - ctx.strm.avail_out;
    _bgzfPack16(dstBegin + 16, len - 1);
 
    dstBegin += len - BLOCK_FOOTER_LENGTH;
    _bgzfPack32(dstBegin, crc32(crc32(0u, NULL, 0u), (Bytef *)(srcBegin), srcLength * sizeof(TSourceValue)));
    _bgzfPack32(dstBegin + 4, srcLength * sizeof(TSourceValue));
 
    return dstCapacity - ctx.strm.avail_out;
}
 
// ----------------------------------------------------------------------------
// Function decompressInit() - GZIP
// ----------------------------------------------------------------------------
 
inline void decompressInit(CompressionContext<detail::gz_compression> & ctx)
{
    int const GZIP_WINDOW_BITS = -15; // no zlib header
 
    ctx.strm.zalloc = NULL;
    ctx.strm.zfree = NULL;
    int status = inflateInit2(&ctx.strm, GZIP_WINDOW_BITS);
    if (status != Z_OK)
        throw io_error("GZip inflateInit2() failed.");
}
 
// ----------------------------------------------------------------------------
// Function decompressInit() - BGZF
// ----------------------------------------------------------------------------
 
inline void decompressInit(CompressionContext<detail::bgzf_compression> & ctx)
{
    decompressInit(static_cast<CompressionContext<detail::gz_compression> &>(ctx));
    ctx.headerPos = 0;
}
 
// ----------------------------------------------------------------------------
// Function _decompressBlock()
// ----------------------------------------------------------------------------
 
template <typename TDestValue, typename TDestCapacity, typename TSourceValue, typename TSourceLength>
inline TDestCapacity _decompressBlock(TDestValue * dstBegin,
                                      TDestCapacity dstCapacity,
                                      TSourceValue * srcBegin,
                                      TSourceLength srcLength,
                                      CompressionContext<detail::bgzf_compression> & ctx)
{
    const size_t BLOCK_HEADER_LENGTH = DefaultPageSize<detail::bgzf_compression>::BLOCK_HEADER_LENGTH;
    const size_t BLOCK_FOOTER_LENGTH = DefaultPageSize<detail::bgzf_compression>::BLOCK_FOOTER_LENGTH;
 
    assert(sizeof(TSourceValue) == 1u);
    assert(sizeof(unsigned) == 4u);
 
    // 1. CHECK HEADER
 
    if (srcLength <= BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH)
        throw io_error("BGZF block too short.");
 
    if (!detail::bgzf_compression::validate_header(std::span{srcBegin, srcLength}))
        throw io_error("Invalid BGZF block header.");
 
    size_t compressedLen = _bgzfUnpack16(srcBegin + 16) + 1u;
    if (compressedLen != srcLength)
        throw io_error("BGZF compressed size mismatch.");
 
    // 2. DECOMPRESS
 
    decompressInit(ctx);
    ctx.strm.next_in = (Bytef *)(srcBegin + BLOCK_HEADER_LENGTH);
    ctx.strm.next_out = (Bytef *)(dstBegin);
    ctx.strm.avail_in = srcLength - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
    ctx.strm.avail_out = dstCapacity * sizeof(TDestValue);
 
    int status = inflate(&ctx.strm, Z_FINISH);
    if (status != Z_STREAM_END)
    {
        inflateEnd(&ctx.strm);
        throw io_error("Inflation failed. Decompressed BGZF data is too big.");
    }
 
    status = inflateEnd(&ctx.strm);
    if (status != Z_OK)
        throw io_error("BGZF inflateEnd() failed.");
 
    // 3. CHECK FOOTER
 
    // Check compressed length in buffer, compute CRC and compare with CRC in buffer.
 
    unsigned crc = crc32(crc32(0u, NULL, 0u), (Bytef *)(dstBegin), dstCapacity - ctx.strm.avail_out);
 
    srcBegin += compressedLen - BLOCK_FOOTER_LENGTH;
    if (_bgzfUnpack32(srcBegin) != crc)
        throw io_error("BGZF wrong checksum.");
 
    if (_bgzfUnpack32(srcBegin + 4) != dstCapacity - ctx.strm.avail_out)
        throw io_error("BGZF size mismatch.");
 
    return (dstCapacity - ctx.strm.avail_out) / sizeof(TDestValue);
}
 
} // namespace seqan3::contrib
 
#endif // defined(SEQAN3_HAS_ZLIB)