Exemplo n.º 1
0
        public string Read(Stream stream)
        {
            int count = stream.Read(_compressedBlock, 0, BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength);

            if (count == 0)
            {
                return(string.Empty);
            }

            if (!BlockGZipStream.HasValidHeader(count, _compressedBlock))
            {
                throw new InvalidDataException("Found an invalid header when reading the GZip block");
            }

            int blockLength = BitConverter.ToUInt16(_compressedBlock, 16) + 1;
            int remaining   = blockLength - BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength;

            count = stream.Read(_compressedBlock, BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength, remaining);

            if (count != remaining)
            {
                throw new InvalidDataException("Found unexpected truncation when reading the GZip block");
            }

            count = _bgzf.Decompress(_compressedBlock, blockLength, _uncompressedBlock, MaxBlockSize);

            if (count < 0)
            {
                throw new CompressionException("Encountered an error when uncompressing the GZip block");
            }
            return(Encoding.UTF8.GetString(_uncompressedBlock, 0, count));
        }
Exemplo n.º 2
0
        //read the next compressed block into provided buffer
        public int ReadCompressedBlock(byte[] buffer)
        {
            if (buffer.Length < BlockGZipStream.BlockGZipFormatCommon.MaxBlockSize)
            {
                throw new InsufficientMemoryException($"Pease provide a buffer at least {BlockGZipStream.BlockGZipFormatCommon.MaxBlockSize} bytes in size.");
            }
            int headerSize = _stream.Read(buffer, 0, BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength);

            // handle the case where no data was read
            if (headerSize == 0)
            {
                return(0);
            }

            // check the header
            if (!BlockGZipStream.HasValidHeader(headerSize, buffer))
            {
                throw new CompressionException($"Found an invalid header when reading the GZip block ({_filePath})");
            }

            int blockLength      = BitConverter.ToUInt16(buffer, 16) + 1;
            int expectedDataSize = blockLength - BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength;

            var dataSize = _stream.Read(buffer, BlockGZipStream.BlockGZipFormatCommon.BlockHeaderLength, expectedDataSize);

            // handle unexpected truncation
            if (expectedDataSize != dataSize)
            {
                throw new CompressionException($"Found unexpected truncation when reading the GZip block ({_filePath})");
            }

            return(headerSize + dataSize);
        }
Exemplo n.º 3
0
        public BgzipTextReader(BlockGZipStream stream, bool leaveOpen = false)
        {
            _leaveOpen = leaveOpen;
            _reader    = new StreamReader(stream, Encoding.UTF8, leaveOpen);

            Type readerType = _reader.GetType();

            _charPosInfo = readerType.GetField("_charPos", BindingFlags.NonPublic | BindingFlags.Instance);
            _charLenInfo = readerType.GetField("_charLen", BindingFlags.NonPublic | BindingFlags.Instance);
        }
Exemplo n.º 4
0
 private BgzipTextWriter(BlockGZipStream bgzipStream) : base(Console.OpenStandardError())
 {
     _buffer      = new byte[BufferSize];
     _bgzipStream = bgzipStream;
 }
Exemplo n.º 5
0
 public BgzipTextWriter(BlockGZipStream stream) : base(stream, Utf8WithoutBom, BufferSize, true)
 {
     _buffer = new byte[BufferSize];
     _stream = stream;
 }