Extend existing two-partner fusion support to ordered multi-gene paths
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics
Research direction
Start by reviewing varcode’s existing variant and effect class structure and how genomic fusions are currently represented. Identify the relevant tests or entry points before defining support for multi-gene fusions; done should mean variant and effect classes represent the requested fusion cases and the behavior is covered by tests.
Written by the indexing model from the issue text.
Description
Current status (2026-10-26; Varcode 10.20.2)
Variant/effect support for two-partner fusions already exists: StructuralVariant represents breakends, GeneFusion / TranslocationToIntergenic represent consequences, and partner-isoform candidates retain distinct transcript interpretations. Supplied RNA structures use make_fusion_outcome, RNAEvidence and load_exacto_fusions. See SV/fusion documentation and RNA imports.
The original request explicitly included multi-gene fusions. Current supplied-fusion imports are linear, two-locus models, and chains of several SVs are not assembled into one allele. Keep this issue open for that residual scope.
Remaining work
Represent an ordered RNA path through more than two source transcript/genomic segments, retaining every junction, orientation, sequence and DNA/RNA link. Reuse the transcript/effect candidate model rather than adding a parallel collection of pairwise fusions that loses the whole path.
Acceptance: a native or independently audited multi-gene example; distinct compatible splice/frame interpretations; explicit partial/unresolved models; source coordinates and read/fragment provenance through serialization; no promotion of local RNA junction support into full-transcript or translation evidence. Coordinate with #259 and the unified composition work in #423.
Original request
Ideally this would allow for multi-gene fusions
- Dominant language
- Python
- Stars
- 88
- Forks
- 28
- Avg merge
- 3h 10m
- Merged PRs (30d)
- 53
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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