/** * Prepare to compress at the given compression level * @param compressionLevel 1 <= compressionLevel <= 9 */ public BlockCompressedOutputStream(final File file, final int compressionLevel) { this.file = file; codec = new BinaryCodec(file, true); deflater = DeflaterFactory.makeDeflater(compressionLevel, true); }
protected BAMFileWriter(final File path, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel); outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
protected BAMFileWriter(final File path) { blockCompressedOutputStream = new BlockCompressedOutputStream(path); outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
/** * Prepare to compress at the given compression level * @param compressionLevel 1 <= compressionLevel <= 9 * @param deflaterFactory custom factory to create deflaters (overrides the default) */ public BlockCompressedOutputStream(final Path path, final int compressionLevel, final DeflaterFactory deflaterFactory) { this.file = path; codec = new BinaryCodec(path, true); deflater = deflaterFactory.makeDeflater(compressionLevel, true); log.debug("Using deflater: " + deflater.getClass().getSimpleName()); }
protected BAMFileWriter(final File path, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
protected BAMFileWriter(final File path) { blockCompressedOutputStream = new BlockCompressedOutputStream(path); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel) { this.file = file; codec = new BinaryCodec(os); if (file != null) { codec.setOutputFileName(file.getAbsolutePath()); } deflater = DeflaterFactory.makeDeflater(compressionLevel, true); }
protected BAMFileWriter(final File path, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, (Path)null, compressionLevel, deflaterFactory); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(absoluteFilename); }
CompressedIndexFileBuffer(File file) { try { mCompressedStream = new BlockCompressedInputStream(file); binaryCodec = new BinaryCodec(mCompressedStream); } catch (IOException ioe) { throw(new RuntimeIOException("Construction error of CSI compressed stream: " + ioe)); } }
protected BAMFileWriter(final OutputStream os, final File file) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file); outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel); outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) { final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null); final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); writeHeader(outputBinaryCodec, samFileHeader); try { blockCompressedOutputStream.flush(); } catch (final IOException ioe) { throw new RuntimeIOException(ioe); } } }
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected BAMFileWriter(final OutputStream os, final File file) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
@Test public void testReadBytesOrFewerNoneAvailable() { final byte[] value = new byte[0]; final ByteArrayInputStream instream = new ByteArrayInputStream(value); final BinaryCodec readCodec = new BinaryCodec(instream); Assert.assertEquals(readCodec.readBytesOrFewer(value, 0, 0), 0); } }
private void init( OutputStream output, SAMFileHeader header, boolean writeHeader) throws IOException { origOutput = output; compressedOut = new BlockCompressedOutputStream(origOutput, null); binaryCodec = new BinaryCodec(compressedOut); recordCodec = new BAMRecordCodec(header); recordCodec.setOutputStream(compressedOut); if (writeHeader) this.writeHeader(header); }