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Migrate default feature-data adapter to tabix-indexed GFF3 - #30

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scottcain merged 2 commits into
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scottcain-switch-to-tabix
Jul 14, 2026
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Migrate default feature-data adapter to tabix-indexed GFF3#30
scottcain merged 2 commits into
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scottcain-switch-to-tabix

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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. 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.

scottcain and others added 2 commits July 14, 2026 13:14
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>
@scottcain
scottcain merged commit e4df5b4 into main Jul 14, 2026
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@scottcain
scottcain deleted the scottcain-switch-to-tabix branch July 14, 2026 20:34
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