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broadinstitute / seqr

web-based analysis tool for rare disease genomics
GNU Affero General Public License v3.0
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wes and wgs samples in hail search #4330

Open jklugherz opened 1 month ago

jklugherz commented 3 weeks ago

@hanars This is still in progress and some tests are failing, but can you take a look and give me some feedback as I continue working on it? I am for sure missing some test cases and probably some edge case handling in the code. It would be helpful if you could point out test cases that I need to add.

Also, I'm changing the variant response structure slightly, namely the genotypes dictionary, so do I have to update the elasticsearch code so that the variant response there matches what's returned from the hail search service?

hanars commented 3 weeks ago

do I have to update the elasticsearch code so that the variant response there matches what's returned from the hail search service?

So a change to the format of the variant is not just a problem for new searches, its a problem for every saved variant ever created. In general, migrating saved variant json is a bad idea and we do not do it. So in fact changing the response of elasticearch will not even solve the problem. I think it would be better to have the UI handle this instead, and work with either the existing structure or the new structure, and only use the new structure for these multi-sample type searches and leave everything else the same

jklugherz commented 6 days ago

@hanars I'm adding test cases and fixing the failing test but in the meantime this PR is ready for your eyes again