Contents
ConvertReferencePanelRule
Convert reference panel rule
ConvertReferencePanelRule handles format conversion only. It resolves a
source panel and runs GenotypeSource$tidy() to reach the requested format,
merging split inputs before writing the converted cached reference panel.
Super class
PolyGenius::Rule -> ConvertReferencePanelRule
Methods
Public methods
ConvertReferencePanelRule$new()ConvertReferencePanelRule$matches()ConvertReferencePanelRule$inputs()ConvertReferencePanelRule$requirements()ConvertReferencePanelRule$run()ConvertReferencePanelRule$clone()
Method new()
Create the conversion rule.
Usage
ConvertReferencePanelRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
ConvertReferencePanelRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
Build dependency inputs.
Usage
ConvertReferencePanelRule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list of dependency specs.
Method requirements()
Declare runtime requirements.
Usage
ConvertReferencePanelRule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification.
inputs — Bound input values.
Returns
Named list with cores and memory.
Method run()
Execute format conversion.
Usage
ConvertReferencePanelRule$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
ConvertReferencePanelRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.