Annotate_Cohort_Upgrade

[Johnnyassaf]

Adding a new optional annotation to the seqr loader pipeline

Proposed Changes

• Changing the Annotate Cohort Function to accept optional additions

Checklist

• Related GitHub Issue created
• Tests covering new change
• Linting checks pass

[MattWellie]

this will work, but for cleanliness can you leave the existing code intact and add an extra method to apply this extra annotation?

AFAIK behind the scenes there's no difference between annotating once with two sources, or annotating twice each with a different source. The fields are all resolved in a lazy way, so it wouldn't be any less efficient to add a second (conditional) mt.annotate_rows() call.

Main reason for implementing this without touching what's already there is so that if something breaks, or something related to this is strange in future, we can use git blame to identify which lines changed, and when, to help debug. If all these lines are changed, it's ambigious whether the new content, or a change to the old content, is responsible for any issues, as they would both be affected by the same change. Adding a new merge commit with just the ~10-20 lines implementing the new functionality is much more useful when trying to track down the source of problems.

[MattWellie]

can you add a version bump to this before we merge it in?

[MattWellie]

AEIOU!