Release 2026.3.0 - #111
Open
bencap wants to merge 16 commits into
Open
Release 2026.3.0#111bencap wants to merge 16 commits into
bencap wants to merge 16 commits into
Conversation
Add `vrs_utils.identify_allele` and `normalize_and_identify`, and switch `vrs_map._construct_vrs_allele` to use them in place of direct `ga4gh_identify` calls. The GA4GH Merkle-tree caches sub-object digests on the object after first identification, so any subsequent mutation (notably the pre-map `refgetAccession` swap, normalization, or state coercion) leaves a stale id unless the cached digests are cleared first. Clearing both the location and allele digests before identification ensures the id always reflects current content. - vrs_utils: new module centralizing the digest-correctness invariant - vrs_map: route both the ref-identical and SNV/delins branches through the new helpers; the ref-identical branch also gains a reassigned `normalize` return value as a side-effect - tests/test_vrs_utils: offline coverage for content-addressing, the stale-digest clearing invariant, the normalize+identify pairing, and the malformed-input error path - align: incidental formatter-driven whitespace tweak
Add MappingOutcome so every (variant, level) record carries a typed outcome, distinguishing a benign absence (intronic, no protein consequence) from a genuine failure that error_message alone cannot convey. Derive the preferred (authoritative) layer from the target's assay level rather than always preferring genomic.
…c projection Select a coding transcript for NC_ protein-coding targets via Ensembl locus overlap plus MANE, so they are no longer silently skipped by reverse translation. Project each measured variant onto its deterministically reachable layers (g<->c, nucleotide->p), emitted as typed-outcome records and routed by preferred_layer_only.
…ferred-layer records - Track represented variant IDs at the preferred layer; re-attribute only variants that have no preferred-layer record, avoiding duplicate mapped_scores for variants with both a dead genomic attempt and a measured protein record (e.g. codon-optimised targets). - Synthesize a preferred-layer failure for variants that mapped only at a non-preferred layer (e.g. wild-type p.= on a genomic-preferred target) so every input variant always has exactly one output record. - Extract _map_protein_layer in vrs_map to return (mapping, reason) instead of an ad-hoc error MappedScore; a row that maps at no layer is failed once, layer-agnostically, carrying the detailed reason. - Add TestNullFailureDedup and TestMapProteinLayerReason test coverage.
…ignments
For protein-vs-DNA BLAT alignments, qcoords always increase (protein
reads N→C regardless of genome strand), so they cannot be used to
detect strand. Switch to tcoords direction for protein queries.
Also normalise hit_subranges and hit_range entries with min/max so
they are always in ascending order, which they are not when the target
gene sits on the minus strand.
- Use tcoords direction (not qcoords) for strand detection when
-q=prot is in blat_params
- Wrap hit_subrange and hit_range endpoints in min/max in both
_get_best_match and align_target_to_protein
_get_mapped_reference_sequence had no CDNA branch, so it fell through to the genomic chromosome lookup and returned the NC_ accession as the post_mapped reference for the cdna layer. This caused target_genes post_mapped_metadata to carry NC_000017.11 under the "cdna" key instead of the NM transcript. Add a CDNA branch that resolves the NM/ENST accession from tx_output.nm (preferred, covers NC_/sequence-based targets) or from the target's own accession when it is already an NM_/ENST (cdna-source targets). Returns None rather than a chromosome when no NM is resolvable. Also adds unit tests for all three layer paths.
…port detailed mapping results
There is no underscore in Ensembl IDs so removing it here.
…rotein-id-check fix: Remove underscore from check for Ensembl Protein ID
…ness feat: VRS Correctness
…ant-projection feat: Reverse Translation Mapping Support
- Reindent the all([...]) call in _offset_target_sequence to hug the brackets instead of nesting the list on its own lines - Bind target = scoreset_metadata.target_genes[target_gene] in select_transcripts to shorten downstream accesses
…unterparts Accession-based targets declared with Ensembl protein (ENSP) or transcript (ENST) accessions previously passed through as bare, unresolved accessions or were dropped, leaving downstream annotation inconsistent with the RefSeq accessions used elsewhere in the pipeline. Resolving them to their RefSeq MANE counterpart keeps output consistent regardless of how the target was declared. - add get_gene_symbol_from_ensembl_protein / _transcript lookups as the bridge from a non-RefSeq accession to get_mane_transcripts_for_gene - add _select_refseq_protein_counterpart / _select_refseq_cdna_counterpart, falling back to the bare accession (protein) or None (cDNA, since np is required on TxSelectResult) when no counterpart resolves - skip standalone VRS mapping for a target with no record group of its own (e.g. base-editor score sets where every row groups under the cDNA target) instead of KeyError'ing on records[target_gene] - re-raise the original alignment error instead of losing its traceback via `raise AlignmentError from e`
identify_allele cleared the cached digests but called ga4gh_identify with the default in_place, which only fills an empty id — and every allele reaching it already has one, minted by AlleleTranslator over un-normalized content. Force recomputation with in_place="always", and recompute location.id separately, since ga4gh_identify writes only the id of the object it is handed. Only deletions and duplications in repeat regions were affected; substitutions normalize to themselves, so their pre-normalization id stayed correct by coincidence and hid the bug. Also look up vrs_ref_allele_seq by extension name rather than extensions[0], which was correct only while it was the sole extension, and compute it only for VRS 1.3 VariationDescriptors — VRS 2.x recovers the reference from refgetAccession and coordinates, so computing it for 2.0 alleles cost a seqrepo fetch per allele for a field nothing reads.
|
coverage: 0.0%. remained the same — mavedb-dev into mavedb-main |
This branch has not been deployed
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
3 participants
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.
Features
MappingOutcomeschema definition andoutcomefield for detailed per-variant mapping resultsBug Fixes
mapped_scoresrecords at the preferred layerMaintenance
.claudeto.gitignore