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package org.broadinstitute.hellbender.engine.spark;
import com.esotericsoftware.kryo.Kryo;
import com.esotericsoftware.kryo.Registration;
import com.esotericsoftware.kryo.serializers.FieldSerializer;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ImmutableMap;
import de.javakaffee.kryoserializers.UnmodifiableCollectionsSerializer;
import de.javakaffee.kryoserializers.guava.ImmutableMapSerializer;
import htsjdk.samtools.*;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.apache.spark.serializer.KryoRegistrator;
import org.bdgenomics.adam.serialization.ADAMKryoRegistrator;
import org.broadinstitute.hellbender.tools.funcotator.FuncotationMap;
import org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation;
import org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata;
import org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils;
import org.broadinstitute.hellbender.utils.Utils;
import org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter;
import org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey;
import org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment;
import org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment;
import org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair;
import org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough;
import org.objenesis.instantiator.ObjectInstantiator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
/**
* GATKRegistrator registers Serializers for our project. We need a JsonSerializer for the Google Genomics classes
* and UnmodifiableCollectionsSerializer from a bug in the version of Kryo we're on.
*/
public class GATKRegistrator implements KryoRegistrator {
private final ADAMKryoRegistrator ADAMregistrator = new ADAMKryoRegistrator();
public GATKRegistrator() {}
/**
* Make sure that all FuncotationMap (which incl. all Funcotation concrete classes and members) classes are registered
* to support {@link org.broadinstitute.hellbender.tools.funcotator.FuncotationMap#create(FuncotationMap)}
*
* @param kryo Kryo instance to update in-place. Never {@code null}
*/
@VisibleForTesting
public static void registerFuncotationMapDependencies(final Kryo kryo) {
Utils.nonNull(kryo);
Registration registration = kryo.register(TableFuncotation.class);
registration.setInstantiator(new ObjectInstantiator() {
public TableFuncotation newInstance() {
return TableFuncotation.create(new LinkedHashMap<>(), Allele.UNSPECIFIED_ALTERNATE_ALLELE, "TEMP", null);
}
});
registration = kryo.register(VcfFuncotationMetadata.class);
registration.setInstantiator(new ObjectInstantiator() {
public VcfFuncotationMetadata newInstance() {
return VcfFuncotationMetadata.create(new ArrayList<>());
}
});
registration = kryo.register(VCFInfoHeaderLine.class);
registration.setInstantiator(new ObjectInstantiator() {
public VCFInfoHeaderLine newInstance() {
return new VCFInfoHeaderLine("TMP", 2, VCFHeaderLineType.String, "");
}
});
registration = kryo.register(Allele.class);
registration.setInstantiator(new ObjectInstantiator() {
public Allele newInstance() {
return Allele.create("TCGA");
}
});
}
@Override
public void registerClasses(Kryo kryo) {
registerGATKClasses(kryo);
// register the ADAM data types using Avro serialization, including:
// AlignmentRecord
// Genotype
// Variant
// DatabaseVariantAnnotation
// NucleotideContigFragment
// Contig
// StructuralVariant
// VariantCallingAnnotations
// VariantEffect
// DatabaseVariantAnnotation
// Dbxref
// Feature
// ReferencePosition
// ReferencePositionPair
// SingleReadBucket
// IndelRealignmentTarget
// TargetSet
// ZippedTargetSet
ADAMregistrator.registerClasses(kryo);
//do this before and after ADAM to try and force our registrations to win out
registerGATKClasses(kryo);
}
@SuppressWarnings({"unchecked", "rawtypes"})
private void registerGATKClasses(Kryo kryo) {
//relatively inefficient serialization of Collections created with Collections.nCopies(), without this
//any Collection created with Collections.nCopies fails to serialize at run time
kryo.register(Collections.nCopies(2, "").getClass(), new FieldSerializer<>(kryo, Collections.nCopies(2, "").getClass()));
// htsjdk.variant.variantcontext.CommonInfo has a Map that defaults to
// a Collections.unmodifiableMap. This can't be handled by the version of kryo used in Spark, it's fixed
// in newer versions (3.0.x), but we can't use those because of incompatibility with Spark. We just include the
// fix here.
// We are tracking this issue with (#874)
kryo.register(Collections.unmodifiableMap(Collections.EMPTY_MAP).getClass(), new UnmodifiableCollectionsSerializer());
kryo.register(Collections.unmodifiableList(Collections.EMPTY_LIST).getClass(), new UnmodifiableCollectionsSerializer());
kryo.register(ImmutableMap.of().getClass(), new ImmutableMapSerializer());
kryo.register(ImmutableMap.of("one","element").getClass(), new ImmutableMapSerializer());
kryo.register(ImmutableMap.of("map","with","multiple","elements").getClass(), new ImmutableMapSerializer());
kryo.register(SAMRecordToGATKReadAdapter.class, new SAMRecordToGATKReadAdapterSerializer());
kryo.register(SAMRecord.class, new SAMRecordSerializer());
kryo.register(BAMRecord.class, new SAMRecordSerializer());
kryo.register(SAMFileHeader.class);
kryo.register(SAMFileHeader.GroupOrder.class);
kryo.register(SAMFileHeader.SortOrder.class);
kryo.register(SAMProgramRecord.class);
kryo.register(SAMReadGroupRecord.class);
kryo.register(EmptyFragment.class, new FieldSerializer(kryo, EmptyFragment.class));
kryo.register(Fragment.class, new FieldSerializer(kryo, Fragment.class));
kryo.register(Pair.class, new Pair.Serializer());
kryo.register(Passthrough.class, new FieldSerializer(kryo, Passthrough.class));
kryo.register(MarkDuplicatesSparkUtils.IndexPair.class, new FieldSerializer(kryo, MarkDuplicatesSparkUtils.IndexPair.class));
kryo.register(ReadsKey.class, new FieldSerializer(kryo, ReadsKey.class));
kryo.register(ReadsKey.KeyForFragment.class, new FieldSerializer(kryo, ReadsKey.KeyForFragment.class));
kryo.register(ReadsKey.KeyForPair.class, new FieldSerializer(kryo, ReadsKey.KeyForPair.class));
}
}
