Hi Filip, thank you for reporting the issue. Its an issue with the AvroTypeInfo. I've pushed a fix to the "master" branch. If you want, you can port your program to 0.9-SNAPSHOT, there, the issue should be fixed.
I'll also push a fix to the "release-0.8" branch if you want to keep using the 0.8 series of Flink. Sorry for the inconvenience. Please let us know if you need more help getting your Flink program to work. Best, Robert On Sun, Mar 15, 2015 at 2:22 PM, Filip Łęczycki <filipleczy...@gmail.com> wrote: > 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 >
