htsjdk.samtools.cram.encoding.external.ExternalByteEncoding 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 is 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.encoding.CRAMCodec;
import htsjdk.samtools.cram.io.BitInputStream;
import htsjdk.samtools.cram.io.BitOutputStream;
import htsjdk.samtools.cram.io.ITF8;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.util.Map;
public class ExternalByteEncoding extends ExternalEncoding {
public ExternalByteEncoding(final int externalBlockContentId) {
super(externalBlockContentId);
}
public static ExternalByteEncoding fromParams(byte[] params) {
final int contentId = ITF8.readUnsignedITF8(params);
return new ExternalByteEncoding(contentId);
}
@Override
public CRAMCodec buildCodec(final BitInputStream coreBlockInputStream,
final BitOutputStream coreBlockOutputStream,
final Map externalBlockInputMap,
final Map externalBlockOutputMap) {
final ByteArrayInputStream inputStream = externalBlockInputMap == null ? null : externalBlockInputMap.get(externalBlockContentId);
final ByteArrayOutputStream outputStream = externalBlockOutputMap == null ? null : externalBlockOutputMap.get(externalBlockContentId);
return new ExternalByteCodec(inputStream, outputStream);
}
}