Skip to content
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.

Sign up for GitHub

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

Jump to bottom

Support VCF annotation ANN field in vcf2adam and adam2vcf #1044

Closed
heuermh opened this issue Jun 5, 2016 · 5 comments
Closed

Support VCF annotation ANN field in vcf2adam and adam2vcf #1044

heuermh opened this issue Jun 5, 2016 · 5 comments
Assignees
@heuermh
Labels
enhancement
Milestone
0.21.0

Comments

@heuermh
Copy link
Member

heuermh commented Jun 5, 2016

Schema were added to bdg-formats in bigdatagenomics/bdg-formats#67.
@heuermh heuermh self-assigned this Jun 5, 2016
@heuermh heuermh mentioned this issue Jun 7, 2016
Closed
61 tasks
@heuermh heuermh mentioned this issue Jul 1, 2016
Closed
@fnothaft fnothaft added this to the 0.20.0 milestone Jul 6, 2016
@fnothaft fnothaft mentioned this issue Jul 6, 2016
Closed
@heuermh heuermh mentioned this issue Jul 6, 2016
Closed
@heuermh heuermh modified the milestones: 0.20.0, 0.22.0, 0.21.0 Oct 13, 2016
@fnothaft
Copy link
Member

fnothaft commented Nov 8, 2016

Should be resolved by #1250.

@heuermh
Copy link
Member Author

heuermh commented Nov 11, 2016

#1250 doesn't fully address this yet.

Mappings between the VCF INFO reserved key ANN and calls to TranscriptEffectConverter.convertToTranscriptEffects and TranscriptEffectConverter.convertToVcfInfoAnnValue need to be added to VariantAnnotationConverter as part of further refactoring.

@heuermh heuermh mentioned this issue Nov 11, 2016
Closed
@jpdna
Copy link
Member

jpdna commented Nov 16, 2016

#1271 should address this correct?

@heuermh
Copy link
Member Author

heuermh commented Nov 16, 2016

No, I haven't written the code yet. :)

Look for a new pull request that says it fixes this issue.

@heuermh
Copy link
Member Author

heuermh commented Jan 5, 2017

Fixed by #1288

@heuermh heuermh closed this as completed Jan 5, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@heuermh heuermh

Labels
enhancement
Projects
None yet
Milestone
0.21.0
Development

No branches or pull requests
3 participants
@heuermh @fnothaft @jpdna