public BGZFCompressionOutputStream(OutputStream out) throws IOException { super(out); this.output = new BlockCompressedOutputStream(out, null); }
public BCFStoppableOutputStream(boolean startStopped, OutputStream out) { super(new BlockCompressedOutputStream(out, null)); origOut = out; stopped = startStopped; }
public BCFStoppableOutputStream(boolean startStopped, OutputStream out) { super(new BlockCompressedOutputStream(out, null)); origOut = out; stopped = startStopped; }
@Override public Writer openStream() throws IOException { return new BufferedWriter(new OutputStreamWriter(new BlockCompressedOutputStream(file))); } };
/** * Writes the index with BGZF. * * @param tabixPath Where to write the index. */ @Override public void write(final Path tabixPath) throws IOException { try(final LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(Files.newOutputStream(tabixPath), (Path)null))) { write(los); } }
/** * Writes the index with BGZF. * * @param tabixPath Where to write the index. */ @Override public void write(final Path tabixPath) throws IOException { try(final LittleEndianOutputStream los = new LittleEndianOutputStream(new BlockCompressedOutputStream(Files.newOutputStream(tabixPath), (Path)null))) { write(los); } }
protected BAMFileWriter(final File path) { blockCompressedOutputStream = new BlockCompressedOutputStream(path); outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
protected BAMFileWriter(final File path) { blockCompressedOutputStream = new BlockCompressedOutputStream(path); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(path.getAbsolutePath()); }
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()); }
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 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 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); }
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); }
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, 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, 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) { blockCompressedOutputStream = new BlockCompressedOutputStream(os, file); outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream); outputBinaryCodec.setOutputFileName(getPathString(file)); }
@Test(groups = "broken") public void testDevNull() throws Exception { final BlockCompressedOutputStream bcos = new BlockCompressedOutputStream("/dev/null"); bcos.write("Hi, Mom!".getBytes()); bcos.close(); }