workspace\(catalogs\)liftoverChains

Liftover Chain Catalog

Description

Inventory and management utility for workspace liftover chain resources.

Details

Inventory and management utility for genome-build liftover chains.

Use this catalog through workspace$catalogs$liftoverChains.

Behavior

  • Exposes the union of downloadable manifest entries and local cache entries.

  • Treats the manifest as read-only.

  • add() and remove() operate only on local cache resources.

Main methods

  • view(): inventory rows with local/downloadable availability.

  • get(from, to): resolve a chain resource reactively (download when missing).

  • add(…) / remove(…): manage only local cached entries.

Methods

Public methods

Method new()

Initialize liftover chain catalog.

Usage 
LiftoverChains$new(manifest.path = NULL)
Arguments
manifest.path

Optional custom manifest CSV path.

Method view()

View the union inventory of local and downloadable chains.

Usage 
LiftoverChains$view()
Returns

data.frame inventory with availability flags.

Method get()

Get liftover chain resource specification(s), optionally executing resolution immediately.

Usage 
LiftoverChains$get(
  from = NULL,
  to = NULL,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)
Arguments
from

Optional source genome build key/name filter.

to

Optional target genome build key/name filter.

.execute

Logical; when TRUE, trigger reactive execution to ensure the requested chain resource(s) are available in cache.

.status

Optional execution-status mode override (“auto”, “yes”, “no”).

Returns

When .execute = TRUE, resolved liftover-chain resource value(s). When .execute = FALSE, a ResourceSpecSet.

Method add()

Add a local liftover chain to the cache.

Usage 
LiftoverChains$add(from, to, path, overwrite = FALSE)
Arguments
from

Source genome build key/name.

to

Target genome build key/name.

path

Existing chain file path.

overwrite

Logical; overwrite existing cached chain if present.

Returns

Invisible ResourceSpec.

Method remove()

Remove cached liftover chains matching optional filters.

Usage 
LiftoverChains$remove(from = NULL, to = NULL)
Arguments
from

Optional source build filter.

to

Optional target build filter.

Returns

Invisible NULL.

Method print()

Print liftover chain inventory summary.

Usage 
LiftoverChains$print(...)
Arguments
…

Unused.