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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Remove redundant references from test data now that we have full-sized references #5313

Open droazen opened 5 years ago

droazen commented 5 years ago

Now that we've added the complete B37 and HG38 references to our test data (https://github.com/broadinstitute/gatk/pull/5309), we should remove redundant snippets of these references to save space, and replace usages of the snippets with usages of the full-sized references.

jonn-smith commented 5 years ago

Funcotator has some separate reference snippets in it, most of which can be removed now.

They're in FuncotatorTestConstants.

As a warning, some of these might not be replaceable and may be used from other tests.

davidbenjamin commented 5 years ago

I'll give this a try.

davidbenjamin commented 5 years ago

@droazen After wrangling with this for a few hours I couldn't quite even get rid of the chr20-21 b37 mini references. There are too many integration tests of deep parts of the engine that I don't feel comfortable messing with. I'm throwing in the towel.

droazen commented 5 years ago

@davidbenjamin Ok, thanks for giving this a try!