Extending MAF limits per issue #276#277
Merged
Merged
Conversation
gregorgorjanc
approved these changes
Jun 2, 2026
gregorgorjanc
left a comment
gregorgorjanc
left a comment
Member
There was a problem hiding this comment.
I think this looks ok, but good if @XingerTang has a look too.
XingerTang
approved these changes
Jun 2, 2026
XingerTang
left a comment
XingerTang
left a comment
Contributor
There was a problem hiding this comment.
Looks really good to me!
Contributor
|
There is a slight increase in the accuracy of the individual accuracy of phased geno prob: original (https://github.com/AlphaGenes/AlphaPeel/actions/runs/26769271139/job/78904016304): new (https://github.com/AlphaGenes/AlphaPeel/actions/runs/26823961490/job/79085999639?pr=277): Generally, most stays the same, but nice to see an actual increase also in the correlation accuracy. |
Member
|
Nice work guys! Squash and merge away. |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What Changed?
Extended the alternative allele frequency limits from [0.01,0.99] to [0.001,0.999] per issue #276.
Small updates to true comparisons in the functional tests for the new limits.
Why this change?
As discussed in #185, to allow potentially higher accuracies and better handling of rare alleles.
Notes/Risks
Minor changes.