openvax / vaxrank / 25014567690
96%
master: 88%

LAST BUILD BRANCH: v3.1.8
DEFAULT BRANCH: master
Ran
Jobs 0
Files 0
Run time –
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
25014567690

push

github

web-flow 
Ship default.yaml + --print-default-config; close last #199 hardcoded item

## Summary

Two related improvements:

1. **Make the last hardcoded scoring item from #199 configurable.** The variant filter at `core_logic.py:150` (silently drop variants with zero mutant-overlapping epitopes) becomes `vaccine_peptides.require_mutant_epitopes_in_variant: bool` (default `true`, preserves legacy behavior). Set `false` to keep every variant a vaccine peptide could be assembled for — useful when the vaxrank report is downstream input for another predictor.

2. **Ship `vaxrank/config/default.yaml`** that documents every YAML knob with its default value. Add `vaxrank --print-default-config` to dump it. Lets users bootstrap a complete starter config:

   ```bash
   vaxrank --print-default-config > my-config.yaml
   # edit what you want
   vaxrank --config my-config.yaml ...
   ```

The default.yaml is grouped by section (`epitopes` / `vaccine_peptides` / `manufacturability`), with comments pointing at DSL syntax for the non-trivial knobs (`filter_expr`, `score_expr`, `default_methods`).

## Status of #199 after this PR

Per the audit, all the items listed in the 2026-04-20 status comment have shipped:
- combined_score formula → `vaccine_peptides.combined_score_mode` (3 modes)
- ranking tuple → `vaccine_peptides.ranking_rules` + `RANKING_RULE_REGISTRY`
- manufacturability rules → `manufacturability.rules` + registry
- manufacturability thresholds → 4 fields in `manufacturability:`
- variant "drop if zero epitopes" filter → **this PR**

I'd recommend closing #199 once this lands.

## Status of #227

Pin bump to varcode 4.x done (in v2.7.0). `apply_variant_to_transcript` from varcode 2.x's MutantTranscript model is used by `mutant_protein_fragment.py`. Zygosity attributes from varcode 2.x are not used anywhere in vaxrank — and don't need to be unless we add a feature that needs them. I'd recommend closing #227 with that note (or splitting zygosity off to its own ticke... (continued)
Source Files on build 25014567690
Detailed source file information is not available for this build.