VariantEffect / dcd_mapping2 / 36777230610

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Build Type

Pull #111

github

Committed by bencap

Commit Message

fix(seqrepo): resolve accession sequences from SeqRepo and commit shared writes

The mapper built accession alleles on whatever sequence cdot assembled from the genome,
and stored it under the accession alias inside a transaction it never committed. For
NM_007294.3 that sequence (7207 nt) is not NCBI's record (7224 nt), so the mapper minted
a different refget, and so a different allele digest, than reverse translation for the
same variant, which left duplicate alleles and broke the convergent/projection labelling.

- seqfetcher() now puts hgvs's SeqRepo-backed SeqFetcher ahead of the FASTA fallback,
  matching the API's chain.
- RefSeq accessions are read from SeqRepo and never written by a mapping run; a missing
  one raises ReferenceSequenceNotFoundError. resolve_refget() requires exactly one
  refget for an accession instead of taking the first of a set.
- A missing Ensembl transcript is assembled from each genome build separately, refused
  unless the builds agree, and stored in SeqRepo without reassigning an existing alias.
- Every mapper write to SeqRepo commits immediately and the SQLite busy timeout is
  raised, so parallel jobs no longer queue behind one process's open transaction.
- Golden tests pin the accession -> refget contract against NCBI records held in a
  fixture that the API repo also carries.

Pull Request Pull Request #111: Release 2026.3.0

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0 of 548 new or added lines in 10 files covered. (0.0%)

34 existing lines in 8 files now uncovered.

0 of 3217 relevant lines covered (0.0%)

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