Founder chromosome-identity qualification

Historical evidence: these measurements retain their recorded revisions, fixtures and limitations; website rendering does not rerun scientific qualification.

Contract correction

The original native founder core keyed SplitMix64 streams by chromosome block position. This qualification covers its intentional replacement with exact UTF-8 chromosome-label identity. Backward compatibility with the defective seeded outputs is not retained. HAPNEST donor, coalescent-age, segment-length, endpoint, phase, and mutation-filtering semantics remain unchanged.

The decisive fixture has three distinguishable chromosomes whose supplied order differs from lexical order, phase-asymmetric donor panels, informative marker patterns, and explicit variant identifiers. Comparisons realign by variant ID and require exact byte equality. It exercises each chromosome alone, forward and reverse orders, surrounding chromosomes, removal and addition of unrelated chromosomes, operational individual batches, changed labels, fixed and different seeds, optional genotype and segment-audit output, and R global-RNG isolation.

Acceptance

Every retained chromosome comparison must report zero H1, H2, genotype, and segment-audit mismatches after coordinate realignment. A changed chromosome label and a changed global seed must each produce a nonzero difference on the informative fixture. Distinct labels must expose distinct native FNV-1a keys, and the fixed known FNV-1a byte fixtures must match exactly. The phase-specific H1/H2 donor fixture and all existing scientific primitive tests remain exact.

Results

All values below were measured from an isolated native installation of the corrected package. Each comparison reports (H1, H2, genotype, audit) mismatches after alignment by explicit chromosome and variant identity.

Comparison	chrZ	01	CHR1
chromosome alone versus forward collection	(0, 0, 0, 0)	(0, 0, 0, 0)	(0, 0, 0, 0)
reversed versus forward collection	(0, 0, 0, 0)	(0, 0, 0, 0)	(0, 0, 0, 0)
surrounded versus forward collection	(0, 0, 0, 0)	(0, 0, 0, 0)	(0, 0, 0, 0)

Removing chromosome 01 produced (0, 0, 0, 0) mismatches on the retained chromosomes. Both operational divisions, 5+7 and 3+4+5 individuals, produced (0, 0, 0, 0) mismatches. Relabelling chrZ changed its output, and changing the seed changed both phases on the informative fixture.

The focused results were 140/140 founder expectations, 80/80 pedigree-meiosis expectations, 51/51 existing gsim() expectations, and 102/102 existing pedigree/record expectations. The isolated native package installation and git diff --check also completed successfully. The known-answer founder fixture was intentionally replaced because the former values encoded the defective block-position stream contract.

Authoritative source