Feature/ybrowse integration#5

Merged

JamesKane merged 16 commits intomainfrom

feature/ybrowse-integration

Dec 10, 2025

Commits on Dec 10, 2025

feat(genomics): Introduce Variant search API and YBrowse VCF ingestion service
JamesKane
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feat(genomics): Add `GenomicsConfig` for reference genome configuration and integrate with ingestion service
JamesKane
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feat(genomics): Add YBrowse variant update system with admin API and scheduled ingestion
JamesKane
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feat(curation): Add TreeCurator role, permissions, audit logging, and curator-centric workflows
JamesKane
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feat(genomics): Add `VariantWithContig` model and integrate contig data into variant workflows
JamesKane
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feat(curation): Add haplogroup-variant association management with UI and audit logging
JamesKane
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feat(genomics): Introduce `VariantGroup` model and integrate logical SNP grouping across application
JamesKane
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feat(curation): Implement haplogroup tree restructuring with merge and split operations
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feat(curation): Enhance haplogroup creation form with tree placement options and validations
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feat(curation): Add support for Y-DNA/mtDNA contig selection and variant liftover
JamesKane
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feat(curation): Add support for editing Variant Groups with shared properties
JamesKane
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feat(curation): Mark regression tests as completed and document Phase 0.5 progress
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feat(curation): Introduce `VariantAlias` support for managing alternative SNP names
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feat(service): Add alias support for variants in haplogroup tree logic and UI
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feat(tree): Add branch age estimates (Formed/TMRCA) to haplogroup tree
JamesKane
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feat(curation): Add variant filtering and count display to haplogroup variants panel
JamesKane
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