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25876601215.2

Pull #167

github

iskandr 
Docs: dedicated pVACseq import guide

New `docs/pvacseq.md` (~260 lines) covers the full read_pvacseq surface
end-to-end:

- What pVACseq is, why import its output (re-score / compare / re-rank
  / combine MHC-I + MHC-II).
- The two TSV flavors (aggregated vs all_epitopes) — what differs,
  how the loader auto-detects.
- Schema mapping table: pVACseq column → topiary column for both
  flavors.
- Derived columns (mhc_class, contains_mutant_residues,
  mutation_start/end_in_peptide, source) — what they are and why
  vaxrank cares.
- Annotation passthroughs naming.
- Worked examples: single-class load, MHC-I + MHC-II concat, filter
  by class with shortcuts and the parsed-string DSL form.
- Per-algorithm scores: the pvacseq_<algo>_<field>_<mtwt> passthrough
  pattern + when to reach for melt_pvacseq_algorithms.
- WT peptide reconstruction (the missense-only path, with the
  HCC1395 292/317 stat).
- Re-scoring with TopiaryPredictor.predict_from_named_peptides via
  the derived peptide dict.
- derive_mhc_class for fresh prediction frames without an
  mhc_class column.
- Metadata stamping — pvacseq_format, kind_support shape.
- Caveats: metrics.json not used, flanking peptides, kind collapsing,
  no CLI.

Wired into mkdocs.yml nav (between Cached Predictions and
Cross-reactivity) and mentioned in docs/index.md's "Multiple input
modes" feature bullet.
Pull Request #167: Add pVACseq report loader (closes #94)

4551 of 5064 relevant lines covered (89.87%)

0.9 hits per line

Source Files on job python-3.12 - 25876601215.2