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Allow variant annotations to be loaded into genotypes #1838

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fnothaft opened this Issue Dec 17, 2017 · 4 comments

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fnothaft commented Dec 17, 2017

In #1771 we stripped variant annotation loading out of genotypes, in favor of keeping the variant annotations stored in the accompanying variant (c.f., VariantContext). However, if you're working with single sample data (e.g., gVCFs), having the variant annotation nested under the genotype may be useful.

@fnothaft fnothaft added this to the 0.24.0 milestone Dec 17, 2017

@fnothaft fnothaft self-assigned this Dec 17, 2017

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heuermh Dec 18, 2017

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What are you thinking for resolving this one? Would it be better to roll back before releasing 0.23.0?

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heuermh commented Dec 18, 2017

What are you thinking for resolving this one? Would it be better to roll back before releasing 0.23.0?

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I don't think we need to resolve this in 0.23.0 (it can wait for 0.24.0, which will follow fairly shortly thereafter), but it winds up being a pretty straightforward fix that adds a configuration flag. I'll have a patch along shortly.

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fnothaft commented Dec 18, 2017

I don't think we need to resolve this in 0.23.0 (it can wait for 0.24.0, which will follow fairly shortly thereafter), but it winds up being a pretty straightforward fix that adds a configuration flag. I'll have a patch along shortly.

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A configuration flag change should probably go in 0.23.0 then, for better or worse folks stick with release versions. We're still waiting on Hadoop-BAM 7.9.1.

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heuermh commented Dec 18, 2017

A configuration flag change should probably go in 0.23.0 then, for better or worse folks stick with release versions. We're still waiting on Hadoop-BAM 7.9.1.

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+1 to that; I just wouldn't want it to drag out the 0.23.0 release is all.

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fnothaft commented Dec 18, 2017

+1 to that; I just wouldn't want it to drag out the 0.23.0 release is all.

fnothaft added a commit to fnothaft/adam that referenced this issue Dec 19, 2017

[ADAM-1838] Make populating variant.annotation field in Genotype conf…
…igurable.

Resolves bigdatagenomics#1838. Modifies the behavior of bigdatagenomics#1771, which disabled populating the
`variant.annotation` field in the `Genotype` record. Now, this field is not
populated by default. To enable populating it, a user can set the property
`org.bdgenomics.adam.converters.VariantContextConverter.NEST_ANN_IN_GENOTYPES`
to true.

@fnothaft fnothaft modified the milestones: 0.24.0, 0.23.0 Dec 19, 2017

heuermh added a commit that referenced this issue Dec 20, 2017

[ADAM-1838] Make populating variant.annotation field in Genotype conf…
…igurable.

Resolves #1838. Modifies the behavior of #1771, which disabled populating the
`variant.annotation` field in the `Genotype` record. Now, this field is not
populated by default. To enable populating it, a user can set the property
`org.bdgenomics.adam.converters.VariantContextConverter.NEST_ANN_IN_GENOTYPES`
to true.

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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