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
