New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 1 commit into from Dec 20, 2017

Conversation

Projects
3 participants
@fnothaft
Member

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.

[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.

@fnothaft fnothaft requested a review from heuermh Dec 19, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone Dec 19, 2017

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins 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.

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

This comment has been minimized.

@heuermh

heuermh Dec 20, 2017

Member

How do we provide conf to the VCFInFormatter?

@heuermh

heuermh Dec 20, 2017

Member

How do we provide conf to the VCFInFormatter?

This comment has been minimized.

@fnothaft

fnothaft Dec 20, 2017

Member

It gets it through the rdd.context.hadoopConfiguration.

@fnothaft

fnothaft Dec 20, 2017

Member

It gets it through the rdd.context.hadoopConfiguration.

@heuermh heuermh merged commit 00ecde1 into bigdatagenomics:master Dec 20, 2017

2 checks passed

Codacy/PR Quality Review Good work! A positive pull request.
Details
default Merged build finished.
Details
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Dec 20, 2017

Member

Thank you, @fnothaft

Member

heuermh commented Dec 20, 2017

Thank you, @fnothaft

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment