tracts.likelihood_options.LikelihoodOptions

class LikelihoodOptions(verbose_log=0, verbose_screen=10, include_autosomes=True, include_allosomes=True)

Bases: object

Logging verbosity and autosome/allosome inclusion flags for a likelihood evaluation.

verbose_log

Log optimization status every verbose_log iterations (0 = never). Defaults to 0.

Type:

int

verbose_screen

Print optimization status every verbose_screen iterations (0 = never). Defaults to 10.

Type:

int

include_autosomes

Whether to include the autosomal log-likelihood in the objective. Defaults to True.

Type:

bool

include_allosomes

Whether to include the allosomal log-likelihood in the objective. Defaults to True.

Type:

bool

include_allosomes: bool = True

include_autosomes: bool = True

with_overrides(**overrides)

Returns a copy of this LikelihoodOptions with the given fields overridden.

Used where include_autosomes/include_allosomes vary per evaluation within a single optimization run (e.g. step 1 evaluates autosomes only, step 2 evaluates allosomes and optionally autosomes), while verbose_log/verbose_screen stay fixed for the whole run.

Return type:

LikelihoodOptions