htsjdk.samtools.cram.compression.GZIPExternalCompressor 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.Defaults;
import htsjdk.samtools.cram.io.InputStreamUtils;
import htsjdk.samtools.cram.structure.block.BlockCompressionMethod;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.RuntimeIOException;
import htsjdk.utils.ValidationUtils;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.zip.Deflater;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
public final class GZIPExternalCompressor extends ExternalCompressor {
// The writeCompressionLevel value is used for write only. When this class is used to read
// (uncompress) data read from a CRAM block, writeCompressionLevel does not necessarily reflect
// the level that was used to compress that data (the compression level that used to create a
// gzip compressed stream is not recovered from Slice block itself).
private final int writeCompressionLevel;
public GZIPExternalCompressor() {
this(Defaults.COMPRESSION_LEVEL);
}
public GZIPExternalCompressor(final int compressionLevel) {
super(BlockCompressionMethod.GZIP);
ValidationUtils.validateArg(compressionLevel >= Deflater.NO_COMPRESSION && compressionLevel <= Deflater.BEST_COMPRESSION,
String.format("Invalid compression level (%d) requested for CRAM GZIP compression", compressionLevel));
this.writeCompressionLevel = compressionLevel;
}
/**
* @return the gzip compression level used by this compressor's compress method
*/
public int getWriteCompressionLevel() { return writeCompressionLevel; }
@Override
public byte[] compress(final byte[] data) {
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
try (final GZIPOutputStream gos = new GZIPOutputStream(byteArrayOutputStream) {
{
def.setLevel(writeCompressionLevel);
}
}) {
IOUtil.copyStream(new ByteArrayInputStream(data), gos);
} catch (final IOException e) {
throw new RuntimeIOException(e);
}
return byteArrayOutputStream.toByteArray();
}
@Override
public byte[] uncompress(byte[] data) {
// Note that when uncompressing data that was retrieved from a (slice) data block
// embedded in a CRAM stream, the writeCompressionLevel value is not recovered
// from the block, and therefore does not necessarily reflect the value that was used
// to compress the data that is now being uncompressed
try (final GZIPInputStream gzipInputStream = new GZIPInputStream(new ByteArrayInputStream(data))) {
return InputStreamUtils.readFully(gzipInputStream);
} catch (final IOException e) {
throw new RuntimeIOException(e);
}
}
@Override
public String toString() {
return String.format("%s(%d)", super.toString(), writeCompressionLevel);
}
}