Module saf 

Site allelele frequency (“SAF”) likelihoods.

SAF likelihoods represent a generalisation of genotype likelihoods from individuals to populations. To estimate the N-dimensional SFS, we need the SAF likelihoods from intersecting sites for those N populations. We represent those by the owned type Saf or the borrowed type SafView, which may represent the full data or only a smaller block of sites.

Modules

iter

Structs and traits for iterating over SAF likelihood matrices and views.

Structs

Saf

Joint SAF likelihood matrix for N populations.

SafView

A view of a joint SAF likelihood matrix for N populations.

ShapeError

An error associated with SAF or SAF site construction using invalid shape.

Site

A single site of SAF likelihoods for N populations.

SiteView

A view of a single site of SAF likelihoods for N populations.

Traits

AsSafView

A type that can be cheaply converted to a SAF view.

AsSiteView

A type that can be cheaply converted to a SAF site.

Lifetime

Stable workaround for lifetime GATs.