Class GzipCodec

java.lang.Object
htsjdk.samtools.util.GzipCodec
public class GzipCodec extends Object
A reusable codec for compressing and decompressing GZIP and BGZF data using direct Deflater/Inflater operations on ByteBuffers. Designed to be allocated once and reused across many compress/decompress operations.

Supports two output formats for compression:

Decompression handles both formats transparently by parsing the FLG byte and skipping any optional GZIP fields.

Not thread-safe. Use one instance per thread.

  • Constructor Details

    • GzipCodec

      public GzipCodec()
      Create a codec with the default compression level and default strategy.

    • GzipCodec

      public GzipCodec(int compressionLevel)
      Create a codec with the specified compression level and default strategy.

    • GzipCodec

      public GzipCodec(int compressionLevel, int deflateStrategy)
      Create a codec with the specified compression level and deflate strategy.

    • GzipCodec

      public GzipCodec(int compressionLevel, int deflateStrategy, DeflaterFactory deflaterFactory, InflaterFactory inflaterFactory)
      Create a codec with full control over compression parameters and factory implementations.
      Parameters:
      compressionLevel - deflate compression level (0-9)
      deflateStrategy - deflate strategy (e.g., Deflater.DEFAULT_STRATEGY, Deflater.FILTERED)
      deflaterFactory - factory for creating Deflater instances
      inflaterFactory - factory for creating Inflater instances

  • Method Details

    • setCheckCrcs

      public void setCheckCrcs(boolean check)
      Enable or disable CRC32 validation during decompression.

    • compress

      public int compress(ByteBuffer input, ByteBuffer output)
      Compress data from input into output using standard GZIP format.
      Parameters:
      input - data to compress (from position to limit; position is advanced to limit)
      output - buffer to write compressed data into (from position; position is advanced)
      Returns:
      number of bytes written to output

    • compress

      public int compress(ByteBuffer input, ByteBuffer output, GzipCodec.Format format)
      Compress data from input into output using the specified format.
      Parameters:
      input - data to compress (from position to limit; position is advanced to limit)
      output - buffer to write compressed data into (from position; position is advanced)
      format - the output format (GzipCodec.Format.GZIP or GzipCodec.Format.BGZF)
      Returns:
      number of bytes written to output

    • compress

      public ByteBuffer compress(ByteBuffer input)
      Compress data and return a new ByteBuffer containing the compressed result.
      Parameters:
      input - data to compress (from position to limit; position is advanced to limit)
      Returns:
      a new ByteBuffer containing the compressed data, positioned at 0 with limit at the end

    • compress

      public ByteBuffer compress(ByteBuffer input, GzipCodec.Format format)
      Compress data and return a new ByteBuffer containing the compressed result.
      Parameters:
      input - data to compress (from position to limit; position is advanced to limit)
      format - the output format
      Returns:
      a new ByteBuffer containing the compressed data, positioned at 0 with limit at the end

    • decompress

      public int decompress(ByteBuffer input, ByteBuffer output)
      Decompress GZIP or BGZF data from input into output. Handles both standard GZIP and BGZF transparently.
      Parameters:
      input - compressed data (from position to limit; position is advanced)
      output - buffer to write decompressed data into (from position; position is advanced)
      Returns:
      number of decompressed bytes written to output

    • decompress

      public ByteBuffer decompress(ByteBuffer input)
      Decompress GZIP or BGZF data and return a new ByteBuffer containing the result. Reads the ISIZE field from the GZIP trailer to determine the output size.
      Parameters:
      input - compressed data (from position to limit; position is advanced)
      Returns:
      a new ByteBuffer containing the decompressed data, positioned at 0 with limit at the end