feat: Reverse Translation Mapping Support#108
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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.
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