@Override
    protected Kryo initialValue() {
      Kryo ret = new Kryo();
      ret.setReferences(true);
      ret.setInstantiatorStrategy(new DefaultInstantiatorStrategy(new StdInstantiatorStrategy()));

      ret.register(Arrays.asList("").getClass(), new ArraysAsListSerializer());
      ret.register(Collections.EMPTY_LIST.getClass(), new CollectionsEmptyListSerializer());
      ret.register(Collections.EMPTY_MAP.getClass(), new CollectionsEmptyMapSerializer());
      ret.register(Collections.EMPTY_SET.getClass(), new CollectionsEmptySetSerializer());
      ret.register(Collections.singletonList("").getClass(), new CollectionsSingletonListSerializer());
      ret.register(Collections.singleton("").getClass(), new CollectionsSingletonSetSerializer());
      ret.register(Collections.singletonMap("", "").getClass(), new CollectionsSingletonMapSerializer());
      ret.register(GregorianCalendar.class, new GregorianCalendarSerializer());
      ret.register(InvocationHandler.class, new JdkProxySerializer());
      UnmodifiableCollectionsSerializer.registerSerializers(ret);
      SynchronizedCollectionsSerializer.registerSerializers(ret);

// custom serializers for non-jdk libs

// register CGLibProxySerializer, works in combination with the appropriate action in handleUnregisteredClass (see below)
      ret.register(CGLibProxySerializer.CGLibProxyMarker.class, new CGLibProxySerializer());
// joda DateTime, LocalDate and LocalDateTime
      ret.register(LocalDate.class, new JodaLocalDateSerializer());
      ret.register(LocalDateTime.class, new JodaLocalDateTimeSerializer());
// guava ImmutableList, ImmutableSet, ImmutableMap, ImmutableMultimap, UnmodifiableNavigableSet
      ImmutableListSerializer.registerSerializers(ret);
      ImmutableSetSerializer.registerSerializers(ret);
      ImmutableMapSerializer.registerSerializers(ret);
      ImmutableMultimapSerializer.registerSerializers(ret);
      return ret;
    }
 

@Override
protected Kryo initialValue() {
  Kryo ret = new Kryo();
  ret.setReferences(true);
  ret.setInstantiatorStrategy(new DefaultInstantiatorStrategy(new StdInstantiatorStrategy()));

  ret.register(Arrays.asList("").getClass(), new ArraysAsListSerializer());
  ret.register(Collections.EMPTY_LIST.getClass(), new CollectionsEmptyListSerializer());
  ret.register(Collections.EMPTY_MAP.getClass(), new CollectionsEmptyMapSerializer());
  ret.register(Collections.EMPTY_SET.getClass(), new CollectionsEmptySetSerializer());
  ret.register(Collections.singletonList("").getClass(), new CollectionsSingletonListSerializer());
  ret.register(Collections.singleton("").getClass(), new CollectionsSingletonSetSerializer());
  ret.register(Collections.singletonMap("", "").getClass(), new CollectionsSingletonMapSerializer());
  ret.register(GregorianCalendar.class, new GregorianCalendarSerializer());
  ret.register(InvocationHandler.class, new JdkProxySerializer());
  UnmodifiableCollectionsSerializer.registerSerializers(ret);
  SynchronizedCollectionsSerializer.registerSerializers(ret);

  // custom serializers for non-jdk libs

  // register CGLibProxySerializer, works in combination with the appropriate action in handleUnregisteredClass (see below)
  ret.register(CGLibProxySerializer.CGLibProxyMarker.class, new CGLibProxySerializer());

  // joda DateTime, LocalDate and LocalDateTime
  ret.register(LocalDate.class, new JodaLocalDateSerializer());
  ret.register(LocalDateTime.class, new JodaLocalDateTimeSerializer());

  // guava ImmutableList, ImmutableSet, ImmutableMap, ImmutableMultimap, UnmodifiableNavigableSet
  ImmutableListSerializer.registerSerializers(ret);
  ImmutableSetSerializer.registerSerializers(ret);
  ImmutableMapSerializer.registerSerializers(ret);
  ImmutableMultimapSerializer.registerSerializers(ret);
  return ret;
}
 

@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<String, Object> 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));
}
 

/**
 * Create our new instance of {@link Kryo}. This is done asynchronously with CompletableFuture
 * so as not to slow down initialization. We save a lot of time this way!
 */
private void serializationInitAsync() {
    kryoInstance = CompletableFuture.supplyAsync(() -> {
        long start = System.currentTimeMillis();

        Kryo kryo = new Kryo();

        // region More serializers

        //noinspection ArraysAsListWithZeroOrOneArgument
        UnmodifiableCollectionsSerializer.registerSerializers(kryo);
        SynchronizedCollectionsSerializer.registerSerializers(kryo);

        ImmutableListSerializer.registerSerializers(kryo);
        ImmutableSetSerializer.registerSerializers(kryo);
        ImmutableMapSerializer.registerSerializers(kryo);
        ImmutableMultimapSerializer.registerSerializers(kryo);
        ImmutableTableSerializer.registerSerializers(kryo);
        ReverseListSerializer.registerSerializers(kryo);
        UnmodifiableNavigableSetSerializer.registerSerializers(kryo);

        ArrayListMultimapSerializer.registerSerializers(kryo);
        HashMultimapSerializer.registerSerializers(kryo);
        LinkedHashMultimapSerializer.registerSerializers(kryo);
        LinkedListMultimapSerializer.registerSerializers(kryo);
        TreeMultimapSerializer.registerSerializers(kryo);
        ArrayTableSerializer.registerSerializers(kryo);
        HashBasedTableSerializer.registerSerializers(kryo);
        TreeBasedTableSerializer.registerSerializers(kryo);

        // endregion

        kryo.register(ConcurrentIndexedCollection.class);
        kryo.register(ShipData.class);
        kryo.register(ShipPositionData.class);
        kryo.register(VSChunkClaim.class);
        kryo.register(HashSet.class);
        kryo.register(UUID.class, new UUIDSerializer());

        // This should be changed to true but only once we're stable
        kryo.setRegistrationRequired(false);

        log.debug("Kryo initialization: " + (System.currentTimeMillis() - start) + "ms");

        return kryo;
    });
}
 

protected Kryo newKryoInstance() {
    Kryo kryo = new Kryo(new DefaultClassResolver(), new CubaMapReferenceResolver());
    kryo.setInstantiatorStrategy(new CubaInstantiatorStrategy());
    if (onlySerializable) {
        kryo.setDefaultSerializer(CubaFieldSerializer.class);
    }

    //To work properly must itself be loaded by the application classloader (i.e. by classloader capable of loading
    //all the other application classes). For web application it means placing this class inside webapp folder.
    kryo.setClassLoader(KryoSerialization.class.getClassLoader());

    //noinspection ArraysAsListWithZeroOrOneArgument
    kryo.register(Arrays.asList("").getClass(), new ArraysAsListSerializer());
    kryo.register(Collections.EMPTY_LIST.getClass(), new CollectionsEmptyListSerializer());
    kryo.register(Collections.EMPTY_MAP.getClass(), new CollectionsEmptyMapSerializer());
    kryo.register(Collections.EMPTY_SET.getClass(), new CollectionsEmptySetSerializer());
    kryo.register(Collections.singletonList("").getClass(), new CollectionsSingletonListSerializer());
    kryo.register(Collections.singleton("").getClass(), new CollectionsSingletonSetSerializer());
    kryo.register(Collections.singletonMap("", "").getClass(), new CollectionsSingletonMapSerializer());
    kryo.register(BitSet.class, new BitSetSerializer());
    kryo.register(GregorianCalendar.class, new GregorianCalendarSerializer());
    kryo.register(InvocationHandler.class, new JdkProxySerializer());
    kryo.register(EnumSet.class, new EnumSetSerializer());
    kryo.register(TreeSet.class, new DefaultSerializers.TreeSetSerializer());
    UnmodifiableCollectionsSerializer.registerSerializers(kryo);
    SynchronizedCollectionsSerializer.registerSerializers(kryo);
    kryo.register(Pattern.class, new RegexSerializer());

    kryo.register(CGLibProxySerializer.CGLibProxyMarker.class, new CGLibProxySerializer());
    ImmutableListSerializer.registerSerializers(kryo);
    ImmutableSetSerializer.registerSerializers(kryo);
    ImmutableMapSerializer.registerSerializers(kryo);
    ImmutableMultimapSerializer.registerSerializers(kryo);
    kryo.register(IndirectList.class, new IndirectContainerSerializer());
    kryo.register(IndirectMap.class, new IndirectContainerSerializer());
    kryo.register(IndirectSet.class, new IndirectContainerSerializer());

    kryo.register(org.eclipse.persistence.indirection.IndirectList.class, new IndirectContainerSerializer());
    kryo.register(org.eclipse.persistence.indirection.IndirectMap.class, new IndirectContainerSerializer());
    kryo.register(org.eclipse.persistence.indirection.IndirectSet.class, new IndirectContainerSerializer());

    //classes with custom serialization methods
    kryo.register(HashMultimap.class, new CubaJavaSerializer());
    kryo.register(ArrayListMultimap.class, new CubaJavaSerializer());
    kryo.register(MetaClassImpl.class, new CubaJavaSerializer());
    kryo.register(MetaPropertyImpl.class, new CubaJavaSerializer());
    kryo.register(UnitOfWorkQueryValueHolder.class, new UnitOfWorkQueryValueHolderSerializer(kryo));

    kryo.addDefaultSerializer(Collection.class, new CubaCollectionSerializer());

    registerEntitySerializer(kryo);

    return kryo;
}