I am trying to use Kryo in spark for the SAMRecord class, but getting the error shown at runtime. I don't understand what this error means, can anyone explain? What do I need to change for Kryo to work with this? The problem is with the member variable mAlignmentBlocks of type List<AlignmentBlock>. Does Kryo have a problem with such lists?
Note that I have registered both AlignmentBlock and SAMRecord by using the following code:
kryo.register(classOf[AlignmentBlock])
kryo.register(classOf[SAMRecord])
And the error I get is this:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException Serialization trace: mAlignmentBlocks (htsjdk.samtools.SAMRecord) at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:626) at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729) at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:42) at com.twitter.chill.Tuple2Serializer.read(TupleSerializers.scala:33) at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729) at org.apache.spark.serializer.KryoDeserializationStream.readObject(KryoSerializer.scala:228) at org.apache.spark.serializer.DeserializationStream.readValue(Serializer.scala:171) at org.apache.spark.serializer.DeserializationStream$$anon$2.getNext(Serializer.scala:201) at org.apache.spark.serializer.DeserializationStream$$anon$2.getNext(Serializer.scala:198) at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73) at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32) at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39) at org.apache.spark.util.collection.ExternalAppendOnlyMap.insertAll(ExternalAppendOnlyMap.scala:152) at org.apache.spark.Aggregator.combineValuesByKey(Aggregator.scala:45) at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:89) at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:98) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306) at org.apache.spark.rdd.RDD.iterator(RDD.scala:270) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
