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HomoeoGWAS v2.1.2
HomoeoGWAS v2.1.2 is a patch release of v2.1.1.
Added: a phenotype screen. Analysed values beyond 5 SD of the mean are listed
by validate_inputs, printed as WARN by fit and interact, recorded under
input_qc.phenotype in the result JSON and flagged by audit
(PHENOTYPE_EXTREME_VALUES, info; beyond 10 SD PHENOTYPE_OUTLIER, review).
Values are never removed.
Added: interact refuses a homoeolog table in which a gene appears in more than
one group of the same subgenome. interact.allow_duplicate_genes: true runs it
anyway; the duplicated genes are recorded and audit flags
DUPLICATED_GROUP_GENES (review).
Documented: with the homoscedastic null the bootstrap random stream differs
with and without checkpointing, so the same seed gives slightly different
Monte Carlo p-values in the two modes.
No statistical code changed. Estimates, p-values and FWER decisions equal
v2.1.1; result JSONs gain an input_qc block. Configs whose homoeolog table
repeats a gene now stop at preflight.