Contents
LiftoverVariantSpaceRule
Liftover variant-space rule
LiftoverVariantSpaceRule handles variant-space requests that are only
available at a different build: lifts a source variant space over to the
requested build via the standard liftover-chain machinery.
Super class
PolyGenius::Rule -> LiftoverVariantSpaceRule
Methods
Public methods
LiftoverVariantSpaceRule$new()LiftoverVariantSpaceRule$matches()LiftoverVariantSpaceRule$inputs()LiftoverVariantSpaceRule$requirements()LiftoverVariantSpaceRule$run()LiftoverVariantSpaceRule$clone()
Method new()
Create the liftover rule.
Usage
LiftoverVariantSpaceRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
LiftoverVariantSpaceRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
Build dependency inputs: the liftover package/binaries, the source-build variant space, and the liftover chain between the source and target builds.
Usage
LiftoverVariantSpaceRule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list of dependency specs.
Method requirements()
Declare runtime requirements.
Usage
LiftoverVariantSpaceRule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification (unused).
inputs — Bound input values (unused).
Returns
Named list with cores and memory.
Method run()
Lift the source variant space over to the target build and
materialize it as variants.bed in the resource's own directory.
Usage
LiftoverVariantSpaceRule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Bound input values from inputs() (source, chain).
logger — Rule-scoped logger for trace/info messages.
Returns
Named list: data (path), meta, logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
LiftoverVariantSpaceRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.