/*
* Copyright 2015-2016 OpenCB
*
* 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 org.opencb.opencga.storage.core.variant.transform;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderVersion;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.VariantFactory;
import org.opencb.biodata.models.variant.VariantSource;
import org.opencb.biodata.models.variant.avro.VariantAvro;
import org.opencb.biodata.tools.variant.stats.VariantGlobalStatsCalculator;
import org.opencb.hpg.bigdata.core.io.avro.AvroEncoder;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
/**
* Created on 01/10/15.
*
* @author Jacobo Coll <jacobo167@gmail.com>
*/
public class VariantAvroTransformTask extends VariantTransformTask<ByteBuffer> {
protected final AvroEncoder<VariantAvro> encoder;
public VariantAvroTransformTask(VariantFactory factory, VariantSource source, Path outputFileJsonFile,
VariantGlobalStatsCalculator variantStatsTask, boolean includesrc) {
super(factory, source, outputFileJsonFile, variantStatsTask, includesrc);
this.encoder = new AvroEncoder<>(VariantAvro.getClassSchema());
}
public VariantAvroTransformTask(VCFHeader header, VCFHeaderVersion version, VariantSource source,
Path outputFileJsonFile, VariantGlobalStatsCalculator variantStatsTask, boolean includeSrc,
boolean generateReferenceBlocks) {
super(header, version, source, outputFileJsonFile, variantStatsTask, includeSrc, generateReferenceBlocks);
this.encoder = new AvroEncoder<>(VariantAvro.getClassSchema());
}
@Override
protected List<ByteBuffer> encodeVariants(List<Variant> variants) {
List<VariantAvro> avros = new ArrayList<>(variants.size());
variants.forEach(variant -> avros.add(variant.getImpl()));
List<ByteBuffer> encoded;
try {
encoded = encoder.encode(avros);
} catch (IOException e) {
throw new RuntimeException(e);
}
return encoded;
}
}