/**
 * Output a curated set of important settings to the logger.
 *
 * May be overridden by subclasses to specify a different set of settings to output.
 */
protected void printSettings() {
    if ( VERBOSITY != Log.LogLevel.DEBUG ) {
        logger.info("HTSJDK Defaults.COMPRESSION_LEVEL : " + Defaults.COMPRESSION_LEVEL);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : " + Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : " + Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS);
        logger.info("HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : " + Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE);
    }
    else {
        // At DEBUG verbosity, print all the HTSJDK defaults:
        Defaults.allDefaults()
                .forEach((key, value) -> logger.info("HTSJDK " + Defaults.class.getSimpleName() + "." + key + " : " + value));
    }

    // Log the configuration options:
    ConfigFactory.logConfigFields(ConfigFactory.getInstance().getGATKConfig(), Log.LogLevel.DEBUG);

    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"));

    logger.info("GCS max retries/reopens: " + BucketUtils.getCloudStorageConfiguration(NIO_MAX_REOPENS, "").maxChannelReopens());
    if (Strings.isNullOrEmpty(NIO_PROJECT_FOR_REQUESTER_PAYS)) {
        logger.info("Requester pays: disabled");
    } else {
        logger.info("Requester pays: enabled. Billed to: " + NIO_PROJECT_FOR_REQUESTER_PAYS);
    }
}
 

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

@Test
public void deflateInflateWithIntel() throws DataFormatException {
    if (!isIntelInflaterDeflaterSupported()) {
        throw new SkipException("IntelInflater/IntelDeflater not available on this platform");
    }

    // create buffers and random input
    final int LEN = 64 * 1024;
    final byte[] input = new RandomDNA().nextBases(LEN);
    final byte[] compressed = new byte[2 * LEN];
    final byte[] result = new byte[LEN];

    final IntelInflaterFactory intelInflaterFactory = new IntelInflaterFactory();
    final IntelDeflaterFactory intelDeflaterFactory = new IntelDeflaterFactory();
    Assert.assertTrue(intelInflaterFactory.usingIntelInflater());
    Assert.assertTrue(intelDeflaterFactory.usingIntelDeflater());

    for (int i = 0; i < 10; i++) {
        // create deflater with compression level i
        final Deflater deflater = intelDeflaterFactory.makeDeflater(i, true);

        // setup deflater
        deflater.setInput(input);
        deflater.finish();

        // compress data
        int compressedBytes = 0;

        // buffer for compressed data is 2x the size of the data we are compressing
        // so this loop should always finish in one iteration
        while (!deflater.finished()) {
            compressedBytes = deflater.deflate(compressed, 0, compressed.length);
        }
        deflater.end();

        // decompress and check output == input
        Inflater inflater = intelInflaterFactory.makeInflater(true);

        inflater.setInput(compressed, 0, compressedBytes);
        inflater.inflate(result);
        inflater.end();

        Assert.assertEquals(input, result);

        // clear compressed and result buffers for next iteration
        Arrays.fill(compressed, (byte)0);
        Arrays.fill(result, (byte)0);
    }
}