Test demonstrating region join failure #1206
Closed
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
In trying to apply shuffleRegionJoin to a use case in gVCF I found that I was getting an OOM error
in running a
InnerShuffleRegionJoin
- on a tiny tiny dataset of 3 variants and 2 variants.In this PR I attempt to recreate the same set of ReferenceRegion intervals in two RDDs to join to demonstrate the problem, here using AlignmentRecords because I modified an existing test.
Its possible that something else is wrong with this test now because I see an ArrayIndexOutofBounds exception rather than OOM, but in any case, the test below is failing for a reason I don't understand - and not gracefully. If we can make this new test work with these intervals, then at least it will be a step towards figuring out why my gVCF join with the same intervals is failing.