How to use

IntelDeflaterFactory

in

com.intel.gkl.compression

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

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"));
}

  IntelDeflaterFactory intelDeflater = new IntelDeflaterFactory();
  writerFactory.setDeflaterFactory(intelDeflater);
  Logger.info("Using intel deflator: " + intelDeflater.usingIntelDeflater());
} else {
  Logger.info("Intel deflater disabled");

BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory());
      ((IntelDeflaterFactory)BlockCompressedOutputStream.getDefaultDeflaterFactory()).usingIntelDeflater());
  final boolean usingIntelInflater = (BlockGunzipper.getDefaultInflaterFactory() instanceof IntelInflaterFactory &&
      ((IntelInflaterFactory)BlockGunzipper.getDefaultInflaterFactory()).usingIntelInflater());

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

BlockCompressedOutputStream.setDefaultDeflaterFactory(new IntelDeflaterFactory());
      ((IntelDeflaterFactory)BlockCompressedOutputStream.getDefaultDeflaterFactory()).usingIntelDeflater());
  final boolean usingIntelInflater = (BlockGunzipper.getDefaultInflaterFactory() instanceof IntelInflaterFactory &&
      ((IntelInflaterFactory)BlockGunzipper.getDefaultInflaterFactory()).usingIntelInflater());