htsjdk.samtools.cram.compression.LZMAExternalCompressor Maven / Gradle / Ivy
/*
* Copyright (c) 2019 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 htsjdk.samtools.cram.compression;
import htsjdk.samtools.cram.io.InputStreamUtils;
import htsjdk.samtools.cram.structure.block.BlockCompressionMethod;
import htsjdk.samtools.util.RuntimeIOException;
import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
public final class LZMAExternalCompressor extends ExternalCompressor {
public LZMAExternalCompressor() {
super(BlockCompressionMethod.LZMA);
}
@Override
public byte[] compress(final byte[] data) {
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(data.length * 2);
try (final XZCompressorOutputStream xzCompressorOutputStream = new XZCompressorOutputStream(byteArrayOutputStream)) {
xzCompressorOutputStream.write(data);
} catch (final IOException e) {
throw new RuntimeIOException(e);
}
return byteArrayOutputStream.toByteArray();
}
@Override
public byte[] uncompress(byte[] data) {
try (final XZCompressorInputStream xzCompressorInputStream = new XZCompressorInputStream(new ByteArrayInputStream(data))) {
return InputStreamUtils.readFully(xzCompressorInputStream);
} catch (final IOException e) {
throw new RuntimeIOException(e);
}
}
}