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Certain Reference Intervals Don't Load With Parquet Predicates #47

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erictu opened this issue Jul 22, 2015 · 3 comments
Open

Certain Reference Intervals Don't Load With Parquet Predicates #47

erictu opened this issue Jul 22, 2015 · 3 comments
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erictu commented Jul 22, 2015

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@erictu erictu added the bug label Jul 22, 2015
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erictu commented Jul 22, 2015

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

@erictu erictu changed the title Reference Doesn't Load For Certain Reference Intervals Certain Reference Intervals Don't Load With Parquet Predicates Jul 22, 2015
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erictu commented Jul 23, 2015

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 bigdatagenomics/bdg-formats#61 and corresponding changes to ADAM.

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

@erictu erictu mentioned this issue Jul 23, 2015
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erictu commented Mar 15, 2016

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

@erictu erictu mentioned this issue Apr 5, 2016
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