htsjdk.samtools.cram.encoding.external.ExternalByteArrayCodec Maven / Gradle / Ivy
/**
* ****************************************************************************
* Copyright 2013 EMBL-EBI
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License inputStream distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* ****************************************************************************
*/
package htsjdk.samtools.cram.encoding.external;
import htsjdk.samtools.cram.io.InputStreamUtils;
import htsjdk.samtools.util.RuntimeIOException;
import java.io.ByteArrayOutputStream;
import java.io.ByteArrayInputStream;
import java.io.IOException;
/**
* Encode Byte Arrays using an External Data Block
*/
public class ExternalByteArrayCodec extends ExternalCodec {
/**
* Construct an External Codec for Byte Arrays
*
* @param inputStream the input bytestream to read from
* @param outputStream the output bytestream to write to
*/
public ExternalByteArrayCodec(final ByteArrayInputStream inputStream,
final ByteArrayOutputStream outputStream) {
super(inputStream, outputStream);
}
@Override
public byte[] read(final int length) {
return InputStreamUtils.readFully(inputStream, length);
}
@Override
public void write(final byte[] object) {
try {
outputStream.write(object);
} catch (IOException e) {
throw new RuntimeIOException(e);
}
}
@Override
public byte[] read() {
throw new RuntimeException("Cannot read byte array of unknown length.");
}
}