Small variant annotation fix #223
Merged
Conversation
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
ch-kr
requested changes
May 11, 2020
Contributor
ch-kr
left a comment
ch-kr
left a comment
There was a problem hiding this comment.
a couple small changes, but looks good to me
gnomad/variant_qc/pipeline.py
Outdated
| :param relationship_col: Column containing the relationship for the sample pair as defined in this module constants. | ||
| :return: A Table with the sibling shared variant counts | ||
| """ | ||
| mt = filter_to_autosomes(mt) |
Contributor
There was a problem hiding this comment.
should we add to the docstring that this currently only runs on autosomes?
Contributor
|
Could you also add a note on the changes to the "Unreleased" section of CHANGELOG.md? That will help users see what changed between releases. |
ch-kr
requested changes
May 11, 2020
Contributor
ch-kr
left a comment
ch-kr
left a comment
There was a problem hiding this comment.
a small comment, also agree with Nick that this should be under ##Unreleased
ch-kr
approved these changes
May 11, 2020
Contributor
ch-kr
left a comment
ch-kr
left a comment
There was a problem hiding this comment.
looks good to me, but I do feel like sib stats and trio stats should be consistent
ch-kr
approved these changes
May 11, 2020
Contributor
ch-kr
left a comment
ch-kr
left a comment
There was a problem hiding this comment.
one small change to the changelog, then looks good to me
ch-kr
approved these changes
May 12, 2020
| if autosomes_only: | ||
| mt = filter_to_autosomes(mt) | ||
| if bi_allelic_only: | ||
| mt = mt.filter_rows(bi_allelic_expr(mt)) |
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Outdated suggestions cannot be applied.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.
No description provided.