- vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every
computed field identical in 2138/2141 samples; the 3 others trace back
to the single-locus raw-intensity rule (K-009); sex rule 1 matches all
- AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3:
new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3,
legacy statistics); the sample summary keeps the real statistics
- NaN sign canonicalised to the x86 pattern (K-014); report P4.md
- tests/unit/test_genotype.py: fuzzy memberships incl. NaN rules, calls
at cluster centres, intensity threshold, BAF/LRR interpolation and
NaN pattern, LogR-dev locus set, sex rules v1/v2, TOP-strand base
calls, invariant dates, end-to-end `simurg genotype` (summary schema,
pass-through columns, thread/layout determinism, overwrite refusal)
- tests/oracle/test_p4_genotype.py: 36 GSA samples x 2 versions
byte-identical to the oracle
- scripts/validate_p4_large.py + cloud task p4: compare every vendor
GTC field by field and as whole files; reports which sex rule matches
kemal