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docs: correct a coverage overstatement in the D34 footnote, and repair the D34 row - #294

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Aug 26, 2026
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docs: correct a coverage overstatement in the D34 footnote, and repair the D34 row#294
Gavin-Borges merged 4 commits into
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docs/d34-coverage-overstatement-and-row-repair

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Three defects, all shipped by PR #291 and all found by an adversarial re-read of that PR's own output against the row it cites. Nothing here is a new claim - each change either removes an assertion or supplies a field the table already required.

1. README.md's competitor-table footnote overstated the pass's coverage

It claimed "Every PredIG/PRIME/NetMHCpan/pVACtools cell above ... is bound to a primary source read in full", and that D34 "lists every source and every cell's citation". It then named ONE exception.

D34 describes TWO. The second is pVACtools's "Pan-allele training" cell, which D34 records as excluded from the verification pass entirely - one research pass had transcribed SESTRAV's own column text into that row - and states plainly is "unchanged and unverified by this pass".

The footnote now says 34 of 36 are source-bound, names both exceptions, and the pVACtools cell is flagged inline in the table the way the NetMHCpan one already was. D34's citations are also per tool, not per cell, so that phrase is dropped.

Note the direction: the overstatement claimed more verification coverage than the pass achieved. That is the flattering direction this repository's defects keep taking, and it is the reason .claude/rules/third-party-claims.md exists.

2. D34's own disposition arithmetic was the root cause, so it is fixed rather than patched around

The row read "seven cells were corrected" plus "Twenty-nine cells were checked and confirmed accurate", which sums to exactly the 36 cells in scope - leaving no slot for the one unresolved cell and the one excluded cell the same row goes on to describe. The arithmetic asserted full coverage while the prose disclosed two gaps, and the README sentence was written from the arithmetic.

Corrected to 7 corrected + 27 confirmed + 1 unresolved + 1 excluded = 36, with a dated note recording the double-booking and its propagation.

3. The D34 table row was malformed: 8 cells against the table's 9 columns

Every field from "Scope boundary" onward rendered one column to the left - the 2026-08-25 date displayed under "Limitation / corrective language", and the file list under "Last verified".

  • Counted escape-aware; the row contains escaped pipes, so a naive pipe count misreads it.
  • Confirmed present on origin/main at fce43b5 before this change rather than introduced by it.

The missing "Scope boundary" cell is supplied, stating only what the row already evidences: the 36 competitor cells across nine capability rows, with SESTRAV's own column and the Tier A metric row explicitly out of scope.

Verification

  • Integrity harness after these edits: 150 PASS / 0 WARN / 2 FAIL / 7 SKIP - unchanged from the pre-edit baseline. The two FAILs are the standing owner-owned C1/D20 and C2/D21 rulings and are untouched here.
  • Table column counts re-checked escape-aware: D34 now 9 cells, matching D31/D32/D33 and the header.
  • No banned non-ASCII introduced in either file.
  • Full local pre-push test gate passed.

Still owner-owned, deliberately not changed here

The NetMHCpan "Multi-virus support" (Pan-pathogen) cell remains unresolved pending your ruling. Per rule 3 of third-party-claims.md, the right replacement could not be sourced either, so it stays flagged rather than rewritten to a synthesized claim.

…r the D34 row

Three defects, all shipped by PR #291 and all found by an adversarial re-read of
that PR's own output against the row it cites.

1. README.md's competitor-table footnote claimed "Every PredIG/PRIME/NetMHCpan/
   pVACtools cell above ... is bound to a primary source read in full" and named
   ONE exception. D34 describes TWO. The second is pVACtools's "Pan-allele
   training" cell, which D34 records as excluded from the verification pass
   entirely - one research pass had transcribed SESTRAV's own column text into
   that row - and states plainly is "unchanged and unverified by this pass".
   The footnote now says 34 of 36 are source-bound and names both exceptions,
   and the pVACtools cell is flagged inline in the table the way the NetMHCpan
   one already was. Note the direction: the overstatement claimed more
   verification coverage than the pass achieved, which is the flattering
   direction this repository's defects keep taking.

2. D34's own disposition arithmetic produced that overstatement and is the root
   cause, so it is fixed rather than patched around. The row read "seven cells
   were corrected" plus "Twenty-nine cells were checked and confirmed accurate",
   which sums to exactly the 36 cells in scope and so left no slot for the one
   unresolved cell and the one excluded cell the same row goes on to describe.
   Corrected to 7 + 27 + 1 + 1 = 36, with a dated note recording that the prior
   accounting double-booked two cells and that the README sentence was written
   from it.

3. The D34 table row was malformed: 8 cells against the table's 9 columns, so
   every field from "Scope boundary" onward rendered one column to the left -
   the 2026-08-25 date displayed under "Limitation / corrective language" and
   the file list under "Last verified". Counted escape-aware (the row contains
   escaped pipes, so a naive pipe count misreads it), and confirmed present on
   origin/main at fce43b5 before this change rather than introduced by it. The
   missing "Scope boundary" cell is supplied, stating only what the row already
   evidences: the 36 competitor cells across nine capability rows, with
   SESTRAV's own column and the Tier A metric row explicitly out of scope.

Integrity harness re-run after these edits: 150 PASS / 0 WARN / 2 FAIL / 7 SKIP,
unchanged from the pre-edit baseline; the two FAILs are the standing owner-owned
C1/D20 and C2/D21 rulings and are untouched here.

Signed-off-by: Gavin Borges <gavinmborges1104@gmail.com>
@Gavin-Borges
Gavin-Borges merged commit 5a23a4e into main Aug 26, 2026
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@Gavin-Borges
Gavin-Borges deleted the docs/d34-coverage-overstatement-and-row-repair branch August 26, 2026 17:27
Gavin-Borges added a commit that referenced this pull request Aug 26, 2026
…thmetic again

Two register-integrity defects found by an independent audit, both in the
table these affiliation rows live in.

1. D34 and D35 rendered as raw pipe-delimited text, not as table rows. A
   stray blank / --- / blank sequence sat between D11 and D34, which ends a
   markdown table, so every row after it fell out of the table entirely. On
   main that orphaned D34 alone; adding D35 would have orphaned it too.
   Removing the three separator lines rejoins them. The Section 1 table is
   now 35 contiguous rows, D27 through D35, with zero arity mismatches
   against its 9-column header - which also matches the heading's "(D1-D35)"
   range for the first time.

2. D34's disposition arithmetic was wrong a second time, and the first
   correction is what left it wrong. PR #294 moved "twenty-nine confirmed"
   to twenty-seven but left "seven cells were corrected" standing, when the
   row's own "-> corrected" enumeration lists EIGHT changed cells: PredIG x2
   (open-source/pip, pan-allele), PRIME x3 (open-source/pip,
   antigen-processing, pan-allele), NetMHCpan x1 (end-to-end), pVACtools x2
   (end-to-end qualifier, antigen-processing). The corrected split is
   8 + 26 + 1 unresolved + 1 excluded = 36.

   The row now records that it was corrected twice and names the check that
   catches this class - count the enumeration, which is one grep. A
   correction pass is itself a claim-making pass
   (.claude/rules/third-party-claims.md rule 2), and this is the third time
   in this repository that the fix for a false claim carried a fresh one.

Verified: table contiguity and per-row arity re-measured escape-aware (35
rows, 0 mismatches); line-citation gate 63/63 at ceiling; commit-ref gate
205 citations resolve; affiliation gate clean; integrity harness
151 PASS / 0 WARN / 2 FAIL / 7 SKIP.

Signed-off-by: Gavin Borges <gavinmborges1104@gmail.com>
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