workspace$catalogs$liftoverChains

Inventory of the UCSC-style chain files used to convert coordinates between genome builds, keyed by (from, to) build pair. Reached as workspace$catalogs$liftoverChains.

view() and get() see the union of the read-only manifest shipped as inst/extdata/manifest.liftoverChains.csv and whatever is already cached under <workspace$config$root>/liftover.chain/. add() and remove() touch the cache only; the manifest is never written.

A chain is never derived from another chain — a pair the manifest does not ship has no producing rule and cannot be resolved unless it is added locally. The stored form is always a plain, uncompressed chain.chain, whichever door it arrived through, so a repeated get() reads the cache and downloads nothing.

Public methods

• LiftoverChains$new()
• LiftoverChains$view()
• LiftoverChains$get()
• LiftoverChains$add()
• LiftoverChains$remove()
• LiftoverChains$print()

Method new()

Read the liftover-chain manifest and build the catalog.

Usage

LiftoverChains$new(manifest.path = NULL)

Arguments

manifest.path — Character scalar path to a manifest CSV, or NULL (default). NULL reads inst/extdata/manifest.liftoverChains.csv from the installed package. The CSV must carry from, to, url and sha256 columns.

Returns

A new LiftoverChains object. Aborts when the manifest file is absent or is missing any required column.

Method view()

List every chain that is cached locally or downloadable.

Usage

LiftoverChains$view()

Returns

A data.frame, one row per from + to pair, sorted by those two columns, with columns from and to (as display labels from genomeBuilds$label()), id (cache id, NA when not cached), path, url, sha256, available.local, downloadable and availability. sha256 always comes from the manifest, never from a cache row, because the stored chain is the decompressed file and not the .chain.gz the checksum measured. Reads the cache index; nothing is downloaded.

Method get()

Resolve every chain matching the filters, downloading any that is not cached yet.

Usage

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

Arguments

from — Character scalar source build key/name, or NULL (default) to match any source build.

to — Character scalar target build key/name, or NULL (default) to match any target build.

.execute — Logical scalar, default TRUE. When TRUE, run the download rule so each matched chain is present in the cache before returning.

.status — One of "auto", "yes", "no"; default polygenius.option.execution.status(), which is "yes". Execution-status display mode for this call.

Returns

When .execute = TRUE and exactly one chain matched, a named list with one element, path, the cached uncompressed chain.chain; when several matched, a list of such lists. When .execute = FALSE, a ResourceSpecSet, with nothing downloaded. Aborts when no inventory row matches the filters, or when a build string is unrecognized.

Method add()

Register a local chain file as a cached chain.

Usage

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

Arguments

from — Character scalar source build key/name.

to — Character scalar target build key/name.

path — Character scalar path to an existing chain file, plain or gzipped.

overwrite — Logical scalar, default FALSE. When FALSE, an already cached from + to pair aborts the call.

Returns

A ResourceSpec, invisibly. Decompresses the file if needed and writes it atomically as <workspace$config$root>/liftover.chain/<id>/chain.chain with a store index entry — the same identity and the same stored form a downloaded chain gets. Aborts when path does not exist, when the stored file is empty, or when it carries no chain header line.

Method remove()

Delete cached liftover chains matching the given filters.

Usage

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

Arguments

from — Character scalar source build key/name, or NULL (default) to match any source build. An unrecognized build string aborts.

to — Character scalar target build key/name, or NULL (default) to match any target build.

Returns

NULL, invisibly. Deletes each matching resource directory under <workspace$config$root>/liftover.chain/ and its store index rows, and reports the count. Called with no arguments it removes every cached chain. The manifest is untouched, so a removed downloadable chain still appears in view() and get() re-downloads it.

Method print()

Print the chain inventory, one line per pair, marking cached entries against downloadable ones.

Usage

LiftoverChains$print(...)

Arguments

... — Unused. Present for print-method compatibility.

Returns

self, invisibly.

Other catalogs: GenomeBuilds, LDblocks, LDs, ReferencePanels, VariantSpaces, workspace_catalogs