Migrate default feature-data adapter to tabix-indexed GFF3 - #30
Merged
Conversation
Partially addresses https://agr-jira.atlassian.net/browse/KANBAN-1452 - GenericGeneSeqPanel now defaults to a bgzip-compressed, tabix-indexed GFF3 file (adapterType="tabix") instead of the JBrowse 1 NCList format, fixing long genes/transcripts (e.g. DMD) failing to load. The legacy NCList adapter remains available via adapterType="nclist". - Add fetchTranscriptsTabix and a GFF3-to-SimpleFeature helper. - Bump to 2.0.0 (breaking default-adapter change) and add a CHANGELOG. - Update the demo app and README for the new default and add a long-gene regression test. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adding @gmod/tabix/@gmod/gff regenerated yarn.lock, which bumped @typescript-eslint/eslint-plugin and parser from 8.24.1 to 8.38.0 within the same ^8.18.0 range. The newer version's no-unnecessary-condition rule now flags the redundant `?? ""` fallback on ref.textContent, which this project's type resolution already treats as non-nullable. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Partially addresses https://agr-jira.atlassian.net/browse/KANBAN-1452