Sequence-variant corpus: substitution tranche (subs × mod, termini, VCF depth, trypsin cut-sites, MNV, variant-borne mod, double subs)

[trishorts]

Substitution tranche for the sequence-variant corpus

Follows #1084 (L0 corpus) and #1095 (L1 deletions). Test-only. Deepens the executable
spec along the substitution axis with 14 new oracle nodes. Every ExpectedForms
oracle is hand-derived from the domain model (bible), never captured from running
code — so a green run certifies the code matches the intended behavior, and a future
regression turns a node red.

Each node runs through both families already in the fixture:

• Corpus_Node — build XML → LoadProteinXML (variants expand at load) → digest → compare, run twice for determinism.
• Corpus_Node_RoundTrip — same, but the consensus protein is serialized through the real ProteinDbWriter and re-read first, so encode+decode is exercised too.

New nodes

Node	What it pins
S00 / S01 / S02	Substitution before / on / after a PTM. S01 (T→S) pins the D7 case for a residue-specific motif — the phospho drops both positionally and motif-wise (our mod is "on T"; S≠T).
S03 / S04	Substitution at the protein start (pos 1) and end (last residue, in-range boundary — contrast the out-of-range F04).
S05 / S06	VCF substitution passing / failing the minAlleleDepth cutoff (fully VCF-encoded, ApplyVariants depth path).
S07 / S08 / S09	Bottom-up: a substitution moves the trypsin knife — destroy a cut site (K→A), create one (A→K), and block cleavage via the not-before-proline rule (I→P under trypsin|P). First digestion-axis nodes.
S10	Multi-residue MNV (TI→VL) over a begin/end range, equal length (exercises the range apply path for a substitution).
S11	A substitution that carries a mod into the proteoform — V4→T whose new T bears a phospho stored on the variant (SequenceVariation.OneBasedModifications). Reciprocal of F03; the round-trip family gives it real teeth on variant-borne-mod serialization (#1083).
SS00 / SS01	Double substitutions — two independent, and two where one lands on the PTM residue.

Harness changes (test infra only)

• BuildMods now also registers variant-borne mods (a VMOD token on a variant), with the motif taken from the variant residue, de-duplicated by IdWithMotif.
• BuildXml emits the nested <subfeature type="modified residue"> / <subposition> structure for VMOD, and labels VCF substitutions as missense_variant.

Result

62 / 62 green (31 nodes × 2 families). No production code touched.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.50%. Comparing base (525cb7c) to head (89cd245).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1098   +/-   ##
=======================================
  Coverage   91.50%   91.50%           
=======================================
  Files         439      439           
  Lines       53542    53542           
  Branches     6511     6511           
=======================================
  Hits        48995    48995           
  Misses       3275     3275           
  Partials     1272     1272           

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