Flink - Avro - AvroTypeInfo issue - Index out of bounds exception

Posted by Filip Łęczycki on
URL: http://deprecated-apache-flink-user-mailing-list-archive.369.s1.nabble.com/Flink-Avro-AvroTypeInfo-issue-Index-out-of-bounds-exception-tp1001.html

Hi

I have an issue while running the following line while usig flink v 0.8.1 (:

    val asdf = new AvroTypeInfo[AlignmentRecord](classOf[AlignmentRecord])

Alignment record belongs to the package :

org.bdgenomics.formats.avro.AlignmentRecord

http://mvnrepository.com/artifact/org.bdgenomics.bdg-formats/bdg-formats/0.4.0

While trying to run I am receivng following exception:

Exception in thread "main" java.lang.IndexOutOfBoundsException

at org.apache.flink.api.java.typeutils.PojoTypeInfo.getPojoFieldAt(PojoTypeInfo.java:178)

at org.apache.flink.api.java.typeutils.AvroTypeInfo.generateFieldsFromAvroSchema(AvroTypeInfo.java:52)

at org.apache.flink.api.java.typeutils.AvroTypeInfo.<init>(AvroTypeInfo.java:38)

at flinkTest.FlinkBAMReader$.main(FlinkBAMReader.scala:74)

While debugging I have noticed that the generated AvroTypeInfo class has a fields array with 42 elements, while the totalFIelds property has value 52 (please find screenshot attached) which seems to be the cause of the exception. Could you please help me o determine what may be the issue with the parser? Is this some bug in AvroTypeInfo class or the AlignmentRecord class is somehow corrupted?

Best Regards/Pozdrawiam,
Filip Łęczycki