Write consistent column sets to variant information files #330
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
* Update SamplesheetParser.groovy * fix multiple samplesheet error message --------- Co-authored-by: Benjamin Wingfield <bwingfield@ebi.ac.uk>
smlmbrt
approved these changes
Jul 3, 2024
There was a problem hiding this comment.
This should work. Although, it might be more useful to users if within match_variants/match_combine:
- Read pvar header lines
- map header lines to schema, set all other headers to str
- drop non-standard columns
This would also allow us to run the matching directly on non-standard VCFs and make pygscatalog more robust.
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Outdated suggestions cannot be applied.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.
pgscatalog-matchreads pvar files with extra columns it can triggerpolars.exceptions.ComputeError: found more fields than defined in 'Schema'closes #324