Genotypes: per-individual diploid germline (phased recombination + novel alleles) - #5

Merged

MuteJester merged 26 commits into

masterfrom

genotype-modeling

Jun 17, 2026

Commits on Jun 16, 2026

feat(genotype): GeneId + GeneIndex (gene grouping over a pool, no Allele change)
MuteJester
committed
feat(genotype): diploid data model (GeneCopy/Haplotype/Genotype) + gene-weight helpers
MuteJester
committed
feat(genotype): ChoiceValue::Haplotype + GeneId with wire format + replay accessors
MuteJester
committed
feat(genotype): SampleHaplotype/SampleGene/SampleAlleleInSlot choice addresses (additive, v1 policy)
MuteJester
committed
feat(genotype): SampleHaplotypePass (up-front viability filter + phased chromosome draw)
MuteJester
committed
feat(genotype): SampleGenotypePass — phased chromosome+gene+allele in one pass
MuteJester
committed
feat(genotype): push_genotype_recombine PyO3 plan builder (one SampleGenotypePass)
MuteJester
committed
feat(genotype): Python Genotype builder (strict default, permissive fallback, export)
MuteJester
committed
feat(genotype): Experiment.with_genotype + mutual-exclusion/receptor-revision/cartridge guards
MuteJester
committed
feat(genotype): lower with_genotype to phased recombine (push_genotype_recombine)
MuteJester
committed
feat(genotype): stamp subject_id/haplotype provenance + result.genotypes
MuteJester
committed
test(genotype): no-genotype output byte-identical to master baseline (sha256 pin)
MuteJester
committed
test(genotype): deletion, het balance, dead-haplotype productive feasibility
MuteJester
committed
fix(genotype): SampleGenotypePass.parameter_signature + SimulationResult slots pin
MuteJester
committed
fix(genotype): replay ordering, strict/permissive, copy dosage, intra-pass feasibility
MuteJester
committed
fix(genotype): wire cartridge gene usage + compile-time complete-haplotype check
MuteJester
committed
fix(genotype): builder/DSL hardening from review (#6-#11)
MuteJester
committed
test(genotype): V-J phasing linkage across two informative haplotypes
MuteJester
committed
fix(genotype): validate replay support, permissive filter-then-fallback, honest usage
MuteJester
committed
docs(genotype): reword usage comment to not trip the legacy-usage-dict pin
MuteJester
committed
docs(genotype): dedicated guide + TIgGER/IgDiscover detection showcase
MuteJester
committed
docs(genotype): fix builder example — specify gene before one-haplotype deletion; valid duplicate alleles
MuteJester
committed
docs(genotype): add 'More genotype recipes' — richer diploid, duplication, programmatic build, inspection (all executed against live API)
MuteJester
committed
feat(genotype): novel/private alleles (synthesis + effective-refdata injection)
MuteJester
committed
fix(genotype): novel-allele review round — functional validation, gene identity, gapped projection
MuteJester
committed

Commits on Jun 17, 2026

fix(genotype): novel-allele review round 4 — no unplaced leak, arg validation, docs reproducibility
MuteJester
committed

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Genotypes: per-individual diploid germline (phased recombination + novel alleles) - #5

Genotypes: per-individual diploid germline (phased recombination + novel alleles)#5
MuteJester merged 26 commits into
masterfrom
genotype-modeling

Commits on Jun 16, 2026

feat(genotype): GeneId + GeneIndex (gene grouping over a pool, no Allele change)

feat(genotype): diploid data model (GeneCopy/Haplotype/Genotype) + gene-weight helpers

feat(genotype): ChoiceValue::Haplotype + GeneId with wire format + replay accessors

feat(genotype): SampleHaplotype/SampleGene/SampleAlleleInSlot choice addresses (additive, v1 policy)

feat(genotype): SampleHaplotypePass (up-front viability filter + phased chromosome draw)

feat(genotype): SampleGenotypePass — phased chromosome+gene+allele in one pass

feat(genotype): push_genotype_recombine PyO3 plan builder (one SampleGenotypePass)

feat(genotype): Python Genotype builder (strict default, permissive fallback, export)

feat(genotype): Experiment.with_genotype + mutual-exclusion/receptor-revision/cartridge guards

feat(genotype): lower with_genotype to phased recombine (push_genotype_recombine)

feat(genotype): stamp subject_id/haplotype provenance + result.genotypes

test(genotype): no-genotype output byte-identical to master baseline (sha256 pin)

test(genotype): deletion, het balance, dead-haplotype productive feasibility

fix(genotype): SampleGenotypePass.parameter_signature + SimulationResult slots pin

fix(genotype): replay ordering, strict/permissive, copy dosage, intra-pass feasibility

fix(genotype): wire cartridge gene usage + compile-time complete-haplotype check

fix(genotype): builder/DSL hardening from review (#6-#11)

test(genotype): V-J phasing linkage across two informative haplotypes

fix(genotype): validate replay support, permissive filter-then-fallback, honest usage

docs(genotype): reword usage comment to not trip the legacy-usage-dict pin

docs(genotype): dedicated guide + TIgGER/IgDiscover detection showcase

docs(genotype): fix builder example — specify gene before one-haplotype deletion; valid duplicate alleles

docs(genotype): add 'More genotype recipes' — richer diploid, duplication, programmatic build, inspection (all executed against live API)

feat(genotype): novel/private alleles (synthesis + effective-refdata injection)

fix(genotype): novel-allele review round — functional validation, gene identity, gapped projection

Commits on Jun 17, 2026

fix(genotype): novel-allele review round 4 — no unplaced leak, arg validation, docs reproducibility