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[ADAM-1838] Make populating variant.annotation field in Genotype configurable #1839

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@fnothaft
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@fnothaft fnothaft commented Dec 19, 2017

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.

…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.
@fnothaft fnothaft requested a review from heuermh Dec 19, 2017
@fnothaft fnothaft added this to the 0.23.0 milestone Dec 19, 2017
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@AmplabJenkins AmplabJenkins commented Dec 19, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2520/
Test PASSed.

@@ -210,7 +210,7 @@ class VariantContextRDDSuite extends ADAMFunSuite {
val rdd: VariantContextRDD = sc.loadVcf(freebayesVcf)

implicit val tFormatter = VCFInFormatter

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@heuermh

heuermh Dec 20, 2017
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How do we provide conf to the VCFInFormatter?

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@fnothaft

fnothaft Dec 20, 2017
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It gets it through the rdd.context.hadoopConfiguration.

@heuermh heuermh merged commit 00ecde1 into bigdatagenomics:master Dec 20, 2017
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Codacy/PR Quality Review Good work! A positive pull request.
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@heuermh
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@heuermh heuermh commented Dec 20, 2017

Thank you, @fnothaft

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