Contents
LiftoverReferencePanelRule
Liftover reference panel rule
LiftoverReferencePanelRule handles genome-build transformation only. It
resolves a source panel and a liftover chain, then runs
GenotypeSource$lift().
Super class
PolyGenius::Rule -> LiftoverReferencePanelRule
Methods
Public methods
LiftoverReferencePanelRule$new()LiftoverReferencePanelRule$matches()LiftoverReferencePanelRule$inputs()LiftoverReferencePanelRule$requirements()LiftoverReferencePanelRule$run()LiftoverReferencePanelRule$clone()
Method new()
Create the liftover rule.
Usage
LiftoverReferencePanelRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
LiftoverReferencePanelRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
Build dependency inputs.
Usage
LiftoverReferencePanelRule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list of dependency specs.
Method requirements()
Declare runtime requirements.
Usage
LiftoverReferencePanelRule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification.
inputs — Bound input values.
Returns
Named list with cores and memory.
Method run()
Execute genome-build liftover.
Usage
LiftoverReferencePanelRule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Bound input values.
logger — Rule logger.
Returns
Rule result list with data, meta, and logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
LiftoverReferencePanelRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.