openvax / vaxrank / 25389919912
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LENS / pVACseq end-to-end vaccine design + processing-credibility annotation (#262)

* Pepsickle credibility tagging (#249) + LENS field-format fixes (#259, #260)

#249 — Pepsickle credibility tagging
------------------------------------
mhcflurry-presentation already includes a flank-aware processing prior,
so a per-k-mer "presentation score" implicitly captures whether the
ligand would be cleaved out and presented. What it can't tell us:
whether the proteasome would cut INSIDE the ligand (destroying it
before MHC) or whether the C-terminal cut at the ligand's boundary is
clean. Pepsickle (Weeder et al., Bioinformatics 2021) gives
per-position cleavage probabilities — we use that as a credibility
filter on existing MHC ligand predictions, not as a separate score
axis.

Each EpitopePrediction gains three optional fields, populated when
``--processing-aware-annotation`` is enabled (default: on):
  - c_term_cleavage_prob: prob of clean release at the C-terminus
  - max_internal_cut_prob: peak cleavage prob strictly inside the
    ligand (high → ligand likely destroyed before MHC)
  - processing_score: composite c_term × (1 − max_internal); 1.0 ideal

Annotation is purely additive — never alters ranking. Surfaced in
HTML / PDF / ASCII per-epitope tables as three extra columns when
populated; absent reports keep their original 6-column shape.

New module: vaxrank/processing.py
  - annotate_processing(predictions, predictor=None) — runs pepsickle
    once per unique source_sequence (not once per peptide); the
    predictor is loaded lazily and degrades gracefully if unavailable
  - _per_position_processing / _composite_processing_score helpers

CLI flag: --processing-aware-annotation / --no-processing-aware-annotation
(default ON).

#259 + #260 — LENS field-format bug fixes
------------------------------------------
Surfaced while running on a real LENS v1.9-dev file (Hugo IPRES Pt10):

#259: variant_coords parser only handled 4-part chr:pos:ref:alt; real
... (continued)
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