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ga4gh / ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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Add filters_applied, filters_passed, and filters_failed to variant #777

Closed heuermh closed 7 years ago

heuermh commented 7 years ago

See https://github.com/ga4gh/schemas/pull/656#issuecomment-272273999

david4096 commented 7 years ago

Thank you kindly! We try to avoid renumbering tags or reusing tag numbers. It's not important that the tag numbers are in order, but if a field hasn't changed its tag number shouldn't change either. This helps guarantee that clients at future versions of the protocol can still handle messages, and field names can be reused safely.

heuermh commented 7 years ago

Got it, I'll fix and rebase

heuermh commented 7 years ago

Addressed review comments and squashed commits.

david4096 commented 7 years ago

This PR is awaiting implementation.

heuermh commented 7 years ago

Sorry, what do you mean by implementation?

Note that if any code implementation relies on htsjdk, it will run into unresolved issue: Genotype requires a method filtersWereApplied (https://github.com/samtools/htsjdk/issues/741)

Let me know if I should rebase and force push to address the necessary merge.

david4096 commented 7 years ago

Hi @heuermh! We look forward to merging this one but need to include it in our existing implementation before we can move forward. Leaving that comment as a reminder to the group that we should implement this sooner, rather than later. That implementation relies on pysam https://github.com/ga4gh/server/issues/1539 .

heuermh commented 7 years ago

I see, thanks!

david4096 commented 7 years ago

Closed in favor of https://github.com/ga4gh/schemas/pull/826

heuermh commented 7 years ago

Thanks!