/** * Note that seek() is not supported if this ctor is used. * @param stream source of bytes */ public BlockCompressedInputStream(final InputStream stream) { this(stream, true, BlockGunzipper.getDefaultInflaterFactory()); }
/** * @param url source of bytes */ public BlockCompressedInputStream(final URL url) { this(url, BlockGunzipper.getDefaultInflaterFactory()); }
/** * @param url source of bytes */ public BlockCompressedInputStream(final URL url) { this(url, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Note that seek() is not supported if this ctor is used. * @param stream source of bytes * @param allowBuffering if true, allow buffering */ public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering) { this(stream, allowBuffering, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Use this ctor if you wish to call seek() * @param file source of bytes * @throws IOException */ public BlockCompressedInputStream(final File file) throws IOException { this(file, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Note that seek() is not supported if this ctor is used. * @param stream source of bytes */ public BlockCompressedInputStream(final InputStream stream) { this(stream, true, BlockGunzipper.getDefaultInflaterFactory()); }
/** * For providing some arbitrary data source. No additional buffering is * provided, so if the underlying source is not buffered, wrap it in a * SeekableBufferedStream before passing to this ctor. * @param strm source of bytes */ public BlockCompressedInputStream(final SeekableStream strm) { this(strm, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Note that seek() is not supported if this ctor is used. * @param stream source of bytes * @param allowBuffering if true, allow buffering */ public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering) { this(stream, allowBuffering, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Use this ctor if you wish to call seek() * @param file source of bytes * @throws IOException */ public BlockCompressedInputStream(final File file) throws IOException { this(file, BlockGunzipper.getDefaultInflaterFactory()); }
/** * For providing some arbitrary data source. No additional buffering is * provided, so if the underlying source is not buffered, wrap it in a * SeekableBufferedStream before passing to this ctor. * @param strm source of bytes */ public BlockCompressedInputStream(final SeekableStream strm) { this(strm, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Note that seek() is not supported if this ctor is used. * @param stream source of bytes * @param allowBuffering if true, allow buffering */ public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering) { this(stream, allowBuffering, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Use this ctor if you wish to call seek() * @param file source of bytes * @throws IOException */ public BlockCompressedInputStream(final File file) throws IOException { this(file, BlockGunzipper.getDefaultInflaterFactory()); }
public AsyncBlockCompressedInputStream(final InputStream stream) { this(stream, BlockGunzipper.getDefaultInflaterFactory()); }
public AsyncBlockCompressedInputStream(final URL url) { this(url, BlockGunzipper.getDefaultInflaterFactory()); }
/** * For providing some arbitrary data source. No additional buffering is * provided, so if the underlying source is not buffered, wrap it in a * SeekableBufferedStream before passing to this ctor. * @param strm source of bytes */ public BlockCompressedInputStream(final SeekableStream strm) { this(strm, BlockGunzipper.getDefaultInflaterFactory()); }
/** * Creates an "empty" factory with no enabled {@link Option}s, {@link ValidationStringency#DEFAULT_STRINGENCY}, * no path wrapper, and {@link htsjdk.samtools.DefaultSAMRecordFactory}. */ public static SamReaderFactory make() { return new SamReaderFactoryImpl(EnumSet.noneOf(Option.class), ValidationStringency.DEFAULT_STRINGENCY, DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory()); }
/** * Creates an "empty" factory with no enabled {@link Option}s, {@link ValidationStringency#DEFAULT_STRINGENCY}, * no path wrapper, and {@link htsjdk.samtools.DefaultSAMRecordFactory}. */ public static SamReaderFactory make() { return new SamReaderFactoryImpl(EnumSet.noneOf(Option.class), ValidationStringency.DEFAULT_STRINGENCY, DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory()); }
public static void setDefaultValidationStringency(final ValidationStringency defaultValidationStringency) { SamReaderFactory.defaultValidationStringency = defaultValidationStringency; // The default may have changed, so reset the default SamReader DEFAULT = new SamReaderFactoryImpl(Option.DEFAULTS, defaultValidationStringency, DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory()); }
public static void setDefaultValidationStringency(final ValidationStringency defaultValidationStringency) { SamReaderFactory.defaultValidationStringency = defaultValidationStringency; // The default may have changed, so reset the default SamReader DEFAULT = new SamReaderFactoryImpl(Option.DEFAULTS, defaultValidationStringency, DefaultSAMRecordFactory.getInstance(), BlockGunzipper.getDefaultInflaterFactory()); }
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")); }