Same-haplotype receptor revision: genotype-aware V replacement - #9

Merged

MuteJester merged 12 commits into

genotype-receptor-revision

Jun 18, 2026

Commits on Jun 17, 2026

feat(engine): AlleleInstance.haplotype provenance field (0/1)
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feat(engine): SampleGenotypePass stamps drawn chromosome on assignments
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feat(engine): genotype-aware ReceptorRevisionPass (same-haplotype candidates, exclude-current, replay validation, signature)
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feat(engine): push_genotype_receptor_revision PyO3 builder with boundary validation
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feat(genotype): receptor_revision(same_haplotype=) DSL + genotype-aware lowering
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feat(genotype): lift genotype+receptor_revision rejection (compile + run_cohort)
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test(genotype): end-to-end genotype-aware receptor revision (truth-based, same-hap, both-hap, novel)
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fix(genotype): genotype-aware receptor revision honors strict post-event contracts; correct run_cohort docstring
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docs(genotype): receptor revision with a genotype + remove from limitations
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test(genotype): update stale pin — genotype+receptor_revision now supported
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Commits on Jun 18, 2026