small functionality patches to strand flip checks, dosage calculator, automated statistics #70
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
| # check that called.alleles is a vector of genotypes in allelic notation or '.' separated by a slash or pipe | ||
| # "*" characters represent overlapping deletions from an upstream indel and are accepted VCF format | ||
| allowed.pattern <- '^((([A-Z]+|\\.|\\*)[/\\|]([A-Z]+|\\.|\\*))|\\.)$' # '|' are special chars in regular expressions | ||
| allowed.pattern <- '^((([A-Z]+|\\.|\\*)[/\\|]([A-Z]+|\\.|\\*))|\\.|[A-Z]+)$' # '|' are special chars in regular expressions |
There was a problem hiding this comment.
You have some comments here about what individual characters mean. Is it possible to include an entire example? I think it would be helpful for interpretation.
Collaborator
Author
There was a problem hiding this comment.
do you mean an example of characters that could be found in a VCF?
There was a problem hiding this comment.
I mean an example of what '^((([A-Z]+|\\.|\\*)[/\\|]([A-Z]+|\\.|\\*))|\\.)$' would look like in the VCF. But if users would know what allelic notation is, I suppose it would not be necessary.
rachelmadang
approved these changes
Feb 20, 2025
rachelmadang
left a comment
rachelmadang
left a comment
There was a problem hiding this comment.
Left a comment for you to think about, but otherwise LGTM!
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Outdated suggestions cannot be applied.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.
Updates to strand flip checker functionality when handling INDELs: mark INDEL effect switches as "effect _switch"
Updates to dosage calculator to handle hemizygous genotypes: single alleles added to allowed allele format list, single alleles evaluated with haploid dosage (+ unit tests).
Updates to
apply.polygenic.scoreto more carefully filter data for statistical analyses.Update version to 3.0.1 (no breaking changes)
I have read the code review guidelines and the code review best practice on GitHub check-list.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added the changes included in this pull request to
NEWSunder the next release version or unreleased, and updated the date.I have updated the version number in
metadata.yamlandDESCRIPTION.Both
R CMD buildandR CMD checkrun successfully.Closes #...
Testing Results
All unit tests pass.