fix: repair SusieFinemapperStep to work with new SL schema and fix lo… #957
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…cus missing the lead variantID
addramir
reviewed
Dec 18, 2024
project-defiant
approved these changes
Dec 19, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
✨ Context
In some cases the SusieFinemapperStep was not correctly assigning the variant with the highest posteriorProbability as the lead. This was because the code was sorting the column as a string instead of as a float/double.
🛠 What does this PR implement
This PR fixes the issue by casting the posteriorProbability column as a double.
Additionally, it also fixes the schema for one of the other functions which was causing issues when 'confidence' was added to the StudyLocus schema. This is a temporary fix to ensure the function works, and a more robust change with tests will be implemented when I tidy up the finemapping step/functions.