/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package net.sf.samtools.util;
import net.sf.samtools.SAMFormatException;
import java.util.zip.Inflater;
import java.util.zip.CRC32;
import java.util.zip.DataFormatException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
/**
* Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].
* The main advantage is that this object can be used over and over again to decompress many blocks,
* whereas a new GZIPInputStream and ByteArrayInputStream would otherwise need to be created for each
* block to be decompressed.
*
* This code requires that the GZIP header conform to the GZIP blocks written to BAM files, with
* a specific subfield and no other optional stuff.
*
* @author alecw@broadinstitute.org
*/
public class BlockGunzipper {
private final Inflater inflater = new Inflater(true); // GZIP mode
private final CRC32 crc32 = new CRC32();
/**
* Decompress GZIP-compressed data
* @param uncompressedBlock must be big enough to hold decompressed output.
* @param compressedBlock compressed data starting at offset 0
* @param compressedLength size of compressed data, possibly less than the size of the buffer.
*/
void unzipBlock(byte[] uncompressedBlock, byte[] compressedBlock, int compressedLength) {
try {
ByteBuffer byteBuffer = ByteBuffer.wrap(compressedBlock, 0, compressedLength);
byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
// Validate GZIP header
if (byteBuffer.get() != BlockCompressedStreamConstants.GZIP_ID1 ||
byteBuffer.get() != (byte)BlockCompressedStreamConstants.GZIP_ID2 ||
byteBuffer.get() != BlockCompressedStreamConstants.GZIP_CM_DEFLATE ||
byteBuffer.get() != BlockCompressedStreamConstants.GZIP_FLG
) {
throw new SAMFormatException("Invalid GZIP header");
}
// Skip MTIME, XFL, OS fields
byteBuffer.position(byteBuffer.position() + 6);
if (byteBuffer.getShort() != BlockCompressedStreamConstants.GZIP_XLEN) {
throw new SAMFormatException("Invalid GZIP header");
}
// Skip blocksize subfield intro
byteBuffer.position(byteBuffer.position() + 4);
// Read ushort
final int totalBlockSize = (byteBuffer.getShort() & 0xffff) + 1;
if (totalBlockSize != compressedLength) {
throw new SAMFormatException("GZIP blocksize disagreement");
}
// Read expected size and CRD from end of GZIP block
final int deflatedSize = compressedLength - BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH - BlockCompressedStreamConstants.BLOCK_FOOTER_LENGTH;
byteBuffer.position(byteBuffer.position() + deflatedSize);
int expectedCrc = byteBuffer.getInt();
int uncompressedSize = byteBuffer.getInt();
inflater.reset();
// Decompress
inflater.setInput(compressedBlock, BlockCompressedStreamConstants.BLOCK_HEADER_LENGTH, deflatedSize);
final int inflatedBytes = inflater.inflate(uncompressedBlock, 0, uncompressedSize);
if (inflatedBytes != uncompressedSize) {
throw new SAMFormatException("Did not inflate expected amount");
}
// Validate CRC
crc32.reset();
crc32.update(uncompressedBlock, 0, uncompressedSize);
final long crc = crc32.getValue();
if ((int)crc != expectedCrc) {
throw new SAMFormatException("CRC mismatch");
}
} catch (DataFormatException e) {
throw new RuntimeException(e);
}
}
}