feat: Center Mappings on VRS Alleles - #773

Closed

bencap wants to merge 21 commits into

release-2026.3.0from

feature/bencap/739/allele-data-model-schema

Commits on Jul 9, 2026

feat(data-providers): add seqrepo-backed vrs data proxy
bencap
committed
fix(vrs): centralize allele id recomputation helpers
bencap
committed
feat(db): add ValidTime mixin for valid-time row versioning
bencap
committed
feat(hgvs): add HGVS accession and cis-phased expression helpers
bencap
committed
feat(vrs): translate cis-phased multivariant HGVS into VRS blocks
bencap
committed
feat(variants): combine cis-phased members into one HGVS expression
bencap
committed
feat(db): add VRS allele closure tables for reverse translation
bencap
committed
chore(types): add mypy stubs for ga4gh and hgvs translation APIs
bencap
committed
build(deps): add variant-annotation as editable sibling dependency
bencap
committed
feat(worker): write mapping job output to the allele closure tables
bencap
committed
fixup into cisphased hgvs commit
bencap
committed
feat(worker): provide a SeqRepo data proxy in the worker context
bencap
committed
fixup into mapper changes
bencap
committed
feat(worker): add reverse translation job for cross-level HGVS alleles
bencap
committed
fix(reverse-translation): anchor cdna transcript lookup to mapping run date
bencap
committed
feat(hgvs): add strip_protein_prediction_parens utility
bencap
committed
fix(vrs-utils): normalize and re-identify VRS alleles to prevent digest collisions
bencap
committed
refactor(reverse-translation): add p. alleles to equivalence set and tighten comments
bencap
committed
feat(mapping): use typed MappingOutcome to distinguish benign skips from failures
bencap
committed
refactor(reverse-translation): replace NullTranscriptSource with live UTA-backed source
bencap
committed
fix(migration): correct down_revision reference in allele closure tables migration
bencap
committed

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feat: Center Mappings on VRS Alleles - #773

feat: Center Mappings on VRS Alleles#773
bencap wants to merge 21 commits into
release-2026.3.0from
feature/bencap/739/allele-data-model-schema

Commits on Jul 9, 2026

feat(data-providers): add seqrepo-backed vrs data proxy

fix(vrs): centralize allele id recomputation helpers

feat(db): add ValidTime mixin for valid-time row versioning

feat(hgvs): add HGVS accession and cis-phased expression helpers

feat(vrs): translate cis-phased multivariant HGVS into VRS blocks

feat(variants): combine cis-phased members into one HGVS expression

feat(db): add VRS allele closure tables for reverse translation

chore(types): add mypy stubs for ga4gh and hgvs translation APIs

build(deps): add variant-annotation as editable sibling dependency

feat(worker): write mapping job output to the allele closure tables

fixup into cisphased hgvs commit

feat(worker): provide a SeqRepo data proxy in the worker context

fixup into mapper changes

feat(worker): add reverse translation job for cross-level HGVS alleles

fix(reverse-translation): anchor cdna transcript lookup to mapping run date

feat(hgvs): add strip_protein_prediction_parens utility

fix(vrs-utils): normalize and re-identify VRS alleles to prevent digest collisions

refactor(reverse-translation): add p. alleles to equivalence set and tighten comments

feat(mapping): use typed MappingOutcome to distinguish benign skips from failures

refactor(reverse-translation): replace NullTranscriptSource with live UTA-backed source

fix(migration): correct down_revision reference in allele closure tables migration