research: AR-001 read/offset accounting with full Yusa validation - #107

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research/assignment-robustness-2026-09

Commits on Sep 6, 2026

research: freeze exploratory assignment-robustness pilot protocol before new experiments
dnncha
committed
28e93cf
research: implement independently checked real-read assignment pilot and provenance
dnncha
committed
c29c12f
research: run bounded public-data pilot with independent validation and retained evidence
dnncha
committed
b6d4b2e
research: add reference forensics and independent reconstruction of multi-offset counting
dnncha
committed
a1d6eef
research: execute source inspection and version-pinned historical-count forensics
dnncha
committed
0a3e06d
research: recognize verified Brunello Seq header and add regression coverage
dnncha
committed
923a329
research: record unsupported comparator version flag and verify Cargo installation instead
dnncha
committed
cc00e5b
research: disclose pilot harness corrections and freeze full-Yusa confirmation scope
dnncha
committed
5196493
research: implement full-archive Yusa confirmation with independent count and event reconstruction
dnncha
committed
5158082
research: execute full checksummed Yusa archives with fail-closed independent validation
dnncha
committed
2780baa
research: freeze Brunello historical-reconstruction lane before execution
dnncha
committed
601ff33
research: reconstruct Brunello multi-offset counts without gene-level inference
dnncha
committed
c822060
research: execute independently reconstructed Brunello historical-prefix audit
dnncha
committed
25df104
research: test an overlap-aware explanation of multi-offset guide aliases
dnncha
committed
ddd2192
research: validate exact-overlap descriptor on both complete guide libraries
dnncha
committed
8aaeca7
research: regenerate descriptive results from verified immutable evidence bundles
dnncha
committed
cfeee6d
research: test corrupted evidence rejection, unsafe paths and trace classifications
dnncha
committed
ed32d3f
research: consolidate offline oracle and evidence-integrity regression gates
dnncha
committed
fea09a1
research: report verified full-archive and prefix findings without biological overclaims
dnncha
committed
fb643b4
research: document completed evidence, one-pass reproduction and publication gates
dnncha
committed
a33aff3
research: preserve aggregate findings and immutable execution artifact identifiers
dnncha
committed
13859bb
research: provide an offline one-command evidence-bundle verification route
dnncha
committed
00ec376
research: verify and retain the final source and findings handoff
dnncha
committed
3a6d381

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research: AR-001 read/offset accounting with full Yusa validation - #107

research: AR-001 read/offset accounting with full Yusa validation#107
dnncha wants to merge 23 commits into
mainfrom
research/assignment-robustness-2026-09

Commits on Sep 6, 2026

research: freeze exploratory assignment-robustness pilot protocol before new experiments

research: implement independently checked real-read assignment pilot and provenance

research: run bounded public-data pilot with independent validation and retained evidence

research: add reference forensics and independent reconstruction of multi-offset counting

research: execute source inspection and version-pinned historical-count forensics

research: recognize verified Brunello Seq header and add regression coverage

research: record unsupported comparator version flag and verify Cargo installation instead

research: disclose pilot harness corrections and freeze full-Yusa confirmation scope

research: implement full-archive Yusa confirmation with independent count and event reconstruction

research: execute full checksummed Yusa archives with fail-closed independent validation

research: freeze Brunello historical-reconstruction lane before execution

research: reconstruct Brunello multi-offset counts without gene-level inference

research: execute independently reconstructed Brunello historical-prefix audit

research: test an overlap-aware explanation of multi-offset guide aliases

research: validate exact-overlap descriptor on both complete guide libraries

research: regenerate descriptive results from verified immutable evidence bundles

research: test corrupted evidence rejection, unsafe paths and trace classifications

research: consolidate offline oracle and evidence-integrity regression gates

research: report verified full-archive and prefix findings without biological overclaims

research: document completed evidence, one-pass reproduction and publication gates

research: preserve aggregate findings and immutable execution artifact identifiers

research: provide an offline one-command evidence-bundle verification route

research: verify and retain the final source and findings handoff