How to use com.intel.gkl.compression

@Override
public void reset() {
  resetNative(nowrap);
  inputBuffer = null;
  inputBufferLength = 0;
  finished = false;
}

/**
 * Returns true if the end of the compressed data output stream has
 * been reached.
 * @return true if the end of the compressed data output stream has
 * been reached
 */
@Override
public int inflate (byte[] b ) {
  return inflateNative( b, 0, b.length);
}

@Override
public void reset() {
  resetNative(nowrap);
  inputBuffer = null;
  inputBufferLength = 0;
  endOfStream = false;
  finished = false;
}

public void initializeCompressionAndDecompression() {
  // Use the Intel Inflater/Deflater for accelerated BAM reading/writing, if possible:
  if (! getArguments().useJdkDeflater) {
    BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory());
  }
  if (! getArguments().useJdkInflater) {
    BlockGunzipper.setDefaultInflaterFactory(new IntelInflaterFactory());
  }
  final boolean usingIntelDeflater = (BlockCompressedOutputStream.getDefaultDeflaterFactory() instanceof IntelDeflaterFactory && ((IntelDeflaterFactory)BlockCompressedOutputStream.getDefaultDeflaterFactory()).usingIntelDeflater());
  logger.info("Deflater: " + (usingIntelDeflater ? "IntelDeflater": "JdkDeflater"));
  final boolean usingIntelInflater = (BlockGunzipper.getDefaultInflaterFactory() instanceof IntelInflaterFactory && ((IntelInflaterFactory)BlockGunzipper.getDefaultInflaterFactory()).usingIntelInflater());
  logger.info("Inflater: " + (usingIntelInflater ? "IntelInflater": "JdkInflater"));
}

public IntelDeflaterFactory(File tmpDir) {
  intelDeflaterSupported = new IntelDeflater().load(tmpDir);
}

 static DeflaterFactory newDeflaterFactory() {
  return new IntelDeflaterFactory();
 }
}

static InflaterFactory newInflatorFactor() {
 return new IntelInflaterFactory();
}
static DeflaterFactory newDeflaterFactory() {

public IntelInflaterFactory(File tmpDir) {
  intelInflaterSupported = new IntelInflater().load(tmpDir);
}

public boolean load() {
  return load(null);
}

/**
 * Closes the compressor and discards any unprocessed input.
 * This method should be called when the compressor is no longer
 * being used, but will also be called automatically by the
 * finalize() method. Once this method is called, the behavior
 * of the IntelDeflater object is undefined.
 */
@Override
public void end() {
  endNative();
}

/**
 * Compresses the input data and fills specified buffer with compressed
 * data. Returns actual number of bytes of compressed data. A return value
 * of 0 indicates that {@link #needsInput() needsInput} should be called
 * in order to determine if more input data is required.
 *
 * @param b the buffer for the compressed data
 * @param off the start offset of the data
 * @param len the maximum number of bytes of compressed data
 * @return the actual number of bytes of compressed data written to the
 *         output buffer
 */
public int deflate(byte[] b, int off, int len ) {
  return deflateNative(b, len);
}

public boolean load(File tmpDir) {
  isSupported = IntelGKLUtils.load(tmpDir);
  if (isSupported) {
    initNative();
  }
  return isSupported;
}

  /**
   * Closes the compressor when garbage is collected.
   */
  protected void finalize() {
    end();
  }
}

  /**
   * Closes the compressor and discards any unprocessed input.
   * This method should be called when the compressor is no longer
   * being used, but will also be called automatically by the
   * finalize() method. Once this method is called, the behavior
   * of the IntelDeflater object is undefined.
   */
  @Override
  public void end() {
    if(lz_stream != 0) {
      endNative();
      lz_stream = 0;
    }
  }
}

 static DeflaterFactory newDeflaterFactory() {
  return new IntelDeflaterFactory();
 }
}

static InflaterFactory newInflatorFactor() {
 return new IntelInflaterFactory();
}
static DeflaterFactory newDeflaterFactory() {

public void reset() {
  logger.debug("Reset deflater");
  resetNative(nowrap);
  inputBuffer = null;
  inputBufferLength = 0;
  endOfStream = false;
  finished = false;
}

  /**
   * Closes the compressor and discards any unprocessed input.
   * This method should be called when the compressor is no longer
   * being used, but will also be called automatically by the
   * finalize() method. Once this method is called, the behavior
   * of the IntelDeflater object is undefined.
   */
  @Override
  public void end() {
    if(lz_stream != 0) {
      endNative();
      lz_stream = 0;
    }
  }
}

/**
 * Compresses the input data and fills specified buffer with compressed
 * data. Returns actual number of bytes of compressed data. A return value
 * of 0 indicates that {@link #needsInput() needsInput} should be called
 * in order to determine if more input data is required.
 *
 * @param b the buffer for the compressed data
 * @param off the start offset of the data
 * @param len the maximum number of bytes of compressed data
 * @return the actual number of bytes of compressed data written to the
 *         output buffer
 */
@Override
public int deflate(byte[] b, int off, int len ) {
  return deflateNative(b, len);
}

/**
 * Compresses the input data and fills specified buffer with compressed
 * data. Returns actual number of bytes of compressed data. A return value
 * of 0 indicates that {@link #needsInput() needsInput} should be called
 * in order to determine if more input data is required.
 *
 * @param b the buffer for the compressed data
 * @param off the start offset of the data
 * @param len the maximum number of bytes of compressed data
 * @return the actual number of bytes of compressed data written to the
 *         output buffer
 */
@Override
public int inflate (byte[] b, int off, int len ) {
  return inflateNative(b, off, len);
}