LiftoverReferencePanelRule

Liftover reference panel rule

Description

Liftover reference panel rule

Liftover reference panel rule

Details

LiftoverReferencePanelRule handles genome-build transformation only. It resolves a source panel and a liftover chain, then runs GenotypeInfo$lift().

Super class

PolyGenius::Rule -> LiftoverReferencePanelRule

Methods

Public methods

• LiftoverReferencePanelRule$new()

• LiftoverReferencePanelRule$matches()

• LiftoverReferencePanelRule$inputs()

• LiftoverReferencePanelRule$requirements()

• LiftoverReferencePanelRule$run()

• LiftoverReferencePanelRule$clone()

Inherited methods

• PolyGenius::Rule$bind()
• PolyGenius::Rule$print()

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Method new()

Create the liftover rule.

Usage

LiftoverReferencePanelRule$new()

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Method matches()

Check whether this rule applies to one output spec.

Usage

LiftoverReferencePanelRule$matches(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Logical.

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Method inputs()

Build dependency inputs.

Usage

LiftoverReferencePanelRule$inputs(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Named list of dependency specs.

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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.

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Method run()

Execute genome-build liftover.

Usage

LiftoverReferencePanelRule$run(output.spec, inputs, logger)

Arguments

output.spec

Output resource specification.

inputs

Bound input values.

logger

Rule logger.

Returns

Rule result list with data, meta, and logs.

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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.