feat: Reverse Translation Mapping Support#108
Draft
bencap wants to merge 3 commits into
Draft
Conversation
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.
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
No description provided.