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broadinstitute
Retain all source IDs on VariantContext merge + test
@bbimber I've added a test to your pr https://github.com/broadinstitute/gatk/pull/8750. Should be good to merge if tests pass.
@lbergelson: this might be permission-related, but despite entering an approving review github is asking for another. I assume that's b/c I dont have write permissions in this project?
@bbimber Hmn, yeah, think it needs someone who has direct write access. I'll get a thumb from a teammate. Thanks for looking at it and for the pr!
Hi @lbergelson and @droazen: it looks like @lbergelson added a limit to avoid excessive sources. Does that satisfy issues remaining on this PR?
Hey @lbergelson, @droazen or @jamesemery: I'm hoping we could finalize this issue. I am unable to commit directly to this branch. To respond to the suggestions from @droazen I made this PR which i am hoping someone can merge into this feature branch (https://github.com/broadinstitute/gatk/pull/8871).
To recap:
- This PR is driven by a request from some of DISCVRseq's users to restore a GATK3 behavior where all source IDs are saved for variants when multiple VCFs are merged.
- This PR would expose this as an opt-in feature, and should not change any default GATK4 behavior. Therefore existing variant merge code should be unchanged.
Hey @lbergelson, @droazen or @jamesemery: sorry to keep bugging you all here, but I'm not sure what else to do here. I'm hoping we can finalize and close out this feature, or identify what is needed to do so. I recapped the state of this PR in my post above.
I could make a clean feature branch with everything in one place if you want; however, if someone with write permissions could simply approve (https://github.com/broadinstitute/gatk/pull/8871) , merge into this branch, and kick off tests that is all I need right now.