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fix: correct stale docs — disagreement threshold, reference set size, SEED-005 exemplar - #64
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- WET_LAB_HANDOFF.md: update max_disagreement for phase3.yaml from 0.30→0.40; both configs now use 0.40 since PR #61 reinstated SEED-008 (Trp-rich puroindoline-a) - METHODS.md §4.4 + §9: correct "45-sequence" → "72-sequence" reference set (amp_curated_references.csv has 72 entries; 45 was pre-expansion count) - DISCOVERY_PREDICTION.md: correct "45-sequence" → "72-sequence" in novelty section; fix SEED-005 exemplar from variant KRFFKKIGSALKFA → actual seed KRLFKKIGSALKFL with note that VAR_009 (KRFFKKIGSALKFA) is the best-ranked variant
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Summary
Post-PR#61 documentation audit found three stale data points that were never updated when SEED-008 was reinstated and configs changed.
max_disagreementtable and troubleshooting text still showed≤ 0.30for phase3.yaml (correct value is 0.40 since PR fix: resolve CRITICAL pre-wetlab pipeline issues (SEED-008 excluded, benchmark config mismatch) #61). The pipeline itself used the correct value; only the handoff guide for wet-lab personnel was wrong.None of these affect synthesis decisions (the pipeline code was correct in all cases). These are documentation-only fixes for scientific reproducibility and wet-lab team communication.
Test plan
amp_curated_references.csvhas 72 sequences (header + 72 data rows)configs/phase3.yamlmax_disagreement = 0.40amp_seeds.csvSEED-005 = KRLFKKIGSALKFL (seed); KRFFKKIGSALKFA is VAR_009 in phase3_ranked🤖 Generated with Claude Code