mango icon indicating copy to clipboard operation
mango copied to clipboard

Published 20 hours ago • verified publisher icon bigdatagenomics

Certain Reference Intervals Don't Load With Parquet Predicates

Open erictu opened this issue 9 years ago • 3 comments

erictu avatar Jul 22 '15 23:07 erictu

Issue is related to parquet filtering. Not providing a parquet predicate works fine

erictu avatar Jul 22 '15 23:07 erictu

Issue is with incorrect Parquet FilterPredicate. NucleotideContigFragment has no length or end field, which does not allow the predicate to be specified correctly. Will be fixed by https://github.com/bigdatagenomics/bdg-formats/pull/61 and corresponding changes to ADAM.

Temporary fix is to use : val pred: FilterPredicate = ((LongColumn("fragmentStartPosition") >= viewRegion.start) || (LongColumn("fragmentStartPosition") <= viewRegion.end))

erictu avatar Jul 23 '15 20:07 erictu

Will be resolved by bigdatagenomics/bdg-formats/#71 and corresponding changes to adam

erictu avatar Mar 15 '16 21:03 erictu