Java SAMTextHeaderCodec.decode方法代码示例

import htsjdk.samtools.SAMTextHeaderCodec; //导入方法依赖的package包/类
private static SAMFileHeader readSAMFileHeader(InputStream inputStream,
		final String id) throws IOException {
	final SecramBlock block = SecramBlock.readFromInputStream(inputStream);

	inputStream = new ByteArrayInputStream(block.getRawContent());

	final ByteBuffer buffer = ByteBuffer.allocate(4);
	buffer.order(ByteOrder.LITTLE_ENDIAN);
	for (int i = 0; i < 4; i++)
		buffer.put((byte) inputStream.read());
	buffer.flip();
	final int size = buffer.asIntBuffer().get();

	final DataInputStream dataInputStream = new DataInputStream(inputStream);
	final byte[] bytes = new byte[size];
	dataInputStream.readFully(bytes);

	final BufferedLineReader bufferedLineReader = new BufferedLineReader(
			new ByteArrayInputStream(bytes));
	final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
	return codec.decode(bufferedLineReader, id);
}
 

import htsjdk.samtools.SAMTextHeaderCodec; //导入方法依赖的package包/类
/**
 * Given an InputStream connected to a fasta dictionary, returns its sequence dictionary
 *
 * Note: does not close the InputStream it's passed
 *
 * @param fastaDictionaryStream InputStream connected to a fasta dictionary
 * @return the SAMSequenceDictionary from the fastaDictionaryStream
 */
public static SAMSequenceDictionary loadFastaDictionary( final InputStream fastaDictionaryStream ) {
    // Don't close the reader when we're done, since we don't want to close the client's InputStream for them
    final BufferedLineReader reader = new BufferedLineReader(fastaDictionaryStream);

    final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
    final SAMFileHeader header = codec.decode(reader, fastaDictionaryStream.toString());

    // Make sure we have a valid sequence dictionary before continuing:
    if (header.getSequenceDictionary() == null || header.getSequenceDictionary().isEmpty()) {
        throw new UserException.MalformedFile (
                "Could not read sequence dictionary from given fasta stream " +
                        fastaDictionaryStream
        );
    }

    return header.getSequenceDictionary();
}
 

import htsjdk.samtools.SAMTextHeaderCodec; //导入方法依赖的package包/类
static SAMFileHeader readHeader(final BinaryCodec stream, final ValidationStringency validationStringency,
		final String source) throws IOException {

	final byte[] buffer = new byte[4];
	stream.readBytes(buffer);
	if (!Arrays.equals(buffer, "BAM\1".getBytes())) {
		throw new IOException("Invalid BAM file header");
	}

	final int headerTextLength = stream.readInt();
	final String textHeader = stream.readString(headerTextLength);
	final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec();
	headerCodec.setValidationStringency(validationStringency);
	final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader), source);

	final int sequenceCount = stream.readInt();
	if (samFileHeader.getSequenceDictionary().size() > 0) {
		// It is allowed to have binary sequences but no text sequences, so
		// only validate if both are present
		if (sequenceCount != samFileHeader.getSequenceDictionary().size()) {
			throw new SAMFormatException("Number of sequences in text header ("
					+ samFileHeader.getSequenceDictionary().size() + ") != number of sequences in binary header ("
					+ sequenceCount + ") for file " + source);
		}
		for (int i = 0; i < sequenceCount; i++) {
			final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(stream, source);
			final SAMSequenceRecord sequenceRecord = samFileHeader.getSequence(i);
			if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) {
				throw new SAMFormatException("For sequence " + i
						+ ", text and binary have different names in file " + source);
			}
			if (sequenceRecord.getSequenceLength() != binarySequenceRecord.getSequenceLength()) {
				throw new SAMFormatException("For sequence " + i
						+ ", text and binary have different lengths in file " + source);
			}
		}
	} else {
		// If only binary sequences are present, copy them into
		// samFileHeader
		final List<SAMSequenceRecord> sequences = new ArrayList<SAMSequenceRecord>(sequenceCount);
		for (int i = 0; i < sequenceCount; i++) {
			sequences.add(readSequenceRecord(stream, source));
		}
		samFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences));
	}

	return samFileHeader;
}
 

import htsjdk.samtools.SAMTextHeaderCodec; //导入方法依赖的package包/类
/**
 * read sam header from file
 * 
 * @param LineReader for htsjdk
 * @return SAMFileHeader
 */
public static SAMFileHeader readHeader(LineReader reader) {
	SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
	SAMFileHeader mHeader = codec.decode(reader, null);
	return mHeader;
}