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BroadcastRegionJoin fails with unmapped reads #821

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arahuja opened this Issue Sep 16, 2015 · 4 comments

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@arahuja
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arahuja commented Sep 16, 2015

This is obvious in hindsight as AlignmentRecord -> ReferenceRegion gives a NullPointerException on unmapped reads.

I opened to the issue to discuss what everyone think the best solution. Things I've thought of are:

  1. Do nothing, assume users will only do this with mapped reads, maybe throw a better warning (as obvious as it is now, I was not clear why this was failing for a while)
  2. Filter unmapped reads for users before they perform the join
  3. Join unmapped regions with some Unmapped region-like placeholder?

2 seems the most reasonable?

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ryan-williams Sep 16, 2015

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This is obvious in hindsight as AlignmentRecord -> ReferenceRegion gives a NullPointerException on unmapped reads.

BRJ doesn't do AlignmentRecord -> ReferenceRegion conversions though, does it?

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ryan-williams commented Sep 16, 2015

This is obvious in hindsight as AlignmentRecord -> ReferenceRegion gives a NullPointerException on unmapped reads.

BRJ doesn't do AlignmentRecord -> ReferenceRegion conversions though, does it?

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arahuja Sep 16, 2015

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No I guess technically not, it's take things keyed by ReferenceRegion so perhaps AlignmentRecord -> ReferenceRegion should fail with a better error? But I could also imagine BRJ doing this automatically and filtering the unmapped reads.

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arahuja commented Sep 16, 2015

No I guess technically not, it's take things keyed by ReferenceRegion so perhaps AlignmentRecord -> ReferenceRegion should fail with a better error? But I could also imagine BRJ doing this automatically and filtering the unmapped reads.

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laserson Sep 16, 2015

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I vote for #1. I'd prefer the join impl not do additional operations that may not be obvious.

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laserson commented Sep 16, 2015

I vote for #1. I'd prefer the join impl not do additional operations that may not be obvious.

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fnothaft Mar 3, 2017

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This is resolved by pending PR #1324. Closing in favor of the main ShuffleRegionJoin ticket #1216.

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fnothaft commented Mar 3, 2017

This is resolved by pending PR #1324. Closing in favor of the main ShuffleRegionJoin ticket #1216.

@fnothaft fnothaft closed this Mar 3, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Mar 8, 2017

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