Java BlockCompressedOutputStream.flush方法代码示例

import htsjdk.samtools.util.BlockCompressedOutputStream; //导入方法依赖的package包/类
/**
 * Block compress input file and create associated tabix index. Newly created file and index are
 * deleted on exit if deleteOnExit true.
 * @throws IOException 
 * @throws InvalidRecordException 
 * */
private void blockCompressAndIndex(String in, String bgzfOut, boolean deleteOnExit) throws IOException, InvalidRecordException {
			
	File inFile= new File(in);
	File outFile= new File(bgzfOut);
	
	LineIterator lin= utils.IOUtils.openURIForLineIterator(inFile.getAbsolutePath());

	BlockCompressedOutputStream writer = new BlockCompressedOutputStream(outFile);
	long filePosition= writer.getFilePointer();
			
	TabixIndexCreator indexCreator=new TabixIndexCreator(TabixFormat.GFF);		
	
	while(lin.hasNext()){
		String line = lin.next();			
		GtfLine gtf= new GtfLine(line.split("\t"));
		writer.write(line.getBytes());
		writer.write('\n');
		indexCreator.addFeature(gtf, filePosition);
		filePosition = writer.getFilePointer();
	}
	writer.flush();
			
	File tbi= new File(bgzfOut + TabixUtils.STANDARD_INDEX_EXTENSION);
	if(tbi.exists() && tbi.isFile()){
		writer.close();
		throw new RuntimeException("Index file exists: " + tbi);
	}
	Index index = indexCreator.finalizeIndex(writer.getFilePointer());
	index.writeBasedOnFeatureFile(outFile);
	writer.close();
	
	if(deleteOnExit){
		outFile.deleteOnExit();
		File idx= new File(outFile.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
		idx.deleteOnExit();
	}
}
 

import htsjdk.samtools.util.BlockCompressedOutputStream; //导入方法依赖的package包/类
/**
 * Private helper method for {@link #convertHeaderlessHadoopBamShardToBam} that takes a SAMFileHeader and writes it
 * to the provided `OutputStream`, correctly encoded for the BAM format and preceded by the BAM magic bytes.
 *
 * @param samFileHeader SAM header to write
 * @param outputStream stream to write the SAM header to
 */
private static void writeBAMHeaderToStream( final SAMFileHeader samFileHeader, final OutputStream outputStream ) {
    final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
    final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));

    final String headerString;
    final Writer stringWriter = new StringWriter();
    new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
    headerString = stringWriter.toString();

    outputBinaryCodec.writeBytes(ReadUtils.BAM_MAGIC);

    // calculate and write the length of the SAM file header text and the header text
    outputBinaryCodec.writeString(headerString, true, false);

    // write the sequences binarily.  This is redundant with the text header
    outputBinaryCodec.writeInt(samFileHeader.getSequenceDictionary().size());
    for (final SAMSequenceRecord sequenceRecord: samFileHeader.getSequenceDictionary().getSequences()) {
        outputBinaryCodec.writeString(sequenceRecord.getSequenceName(), true, true);
        outputBinaryCodec.writeInt(sequenceRecord.getSequenceLength());
    }

    try {
        blockCompressedOutputStream.flush();
    } catch (final IOException ioe) {
        throw new RuntimeIOException(ioe);
    }
}
 

import htsjdk.samtools.util.BlockCompressedOutputStream; //导入方法依赖的package包/类
@Override
public OrderedByteArray apply(OrderedByteArray object) {
	if (object == null)
		throw new NullPointerException();

	log.debug("processing container " + object.order);
	Container container;
	try {
		container = ContainerIO.readContainer(header.getVersion(), new ByteArrayInputStream(object.bytes));
		if (container.isEOF())
			return null;

		ArrayList<CramCompressionRecord> records = new ArrayList<CramCompressionRecord>(container.nofRecords);
		parser.getRecords(container, records, ValidationStringency.SILENT);
		n.normalize(records, null, 0, container.header.substitutionMatrix);

		ByteArrayOutputStream bamBAOS = new ByteArrayOutputStream();
		BlockCompressedOutputStream os = new BlockCompressedOutputStream(bamBAOS, null);
		codec.setOutputStream(os);
		for (CramCompressionRecord record : records) {
			SAMRecord samRecord = f.create(record);
			codec.encode(samRecord);
		}
		os.flush();
		OrderedByteArray bb = new OrderedByteArray();
		bb.bytes = bamBAOS.toByteArray();
		bb.order = object.order;
		log.debug(String.format("Converted OBA %d, records %d", object.order, records.size()));
		return bb;
	} catch (IOException | IllegalArgumentException | IllegalAccessException e) {
		throw new RuntimeException(e);
	}
}
 

import htsjdk.samtools.util.BlockCompressedOutputStream; //导入方法依赖的package包/类
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);
	}
}