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));
}
//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);
}
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);
}
private BgzipTextWriter(BlockGZipStream bgzipStream) : base(Console.OpenStandardError())
{
_buffer = new byte[BufferSize];
_bgzipStream = bgzipStream;
}
public BgzipTextWriter(BlockGZipStream stream) : base(stream, Utf8WithoutBom, BufferSize, true)
{
_buffer = new byte[BufferSize];
_stream = stream;
}