Contents
LiftoverLDBlocksRule
Liftover LD block boundaries rule
LiftoverLDBlocksRule produces a block set for a build that is not published
by lifting the same population's set from a build that is, then re-imposing
the canonical partition.
Complements DownloadLDBlocksRule: ld.blocks.transition() routes each
request to exactly one of them. The published hg38 sets make this rule
dormant for the Berisa-Pickrell populations; it exists for a build or a
population the manifest does not cover.
Strictness
A block that does not lift, changes chromosome, inverts, or lands on a
non-autosomal contig fails the whole lift. Only a block split across contigs
is tolerated, reduced to its majority contig and counted against
PG.LDBLOCKS.LIFT.RECONCILE.MAX.
Measured against UCSC's hg19 to hg38 chain, the Berisa-Pickrell sets do not
satisfy that bar: EUR yields 1699 clean blocks, 3 that change chromosome and
1 on a non-autosomal contig, with 31 of the 1699 needing majority-contig
reconciliation. Nothing is unmapped and nothing inverts. So this rule would
refuse to derive the published hg38 sets, which is why they are published
rather than derived. website/deploy/update-ld-blocks.R built them under a
looser policy: it drops non-autosomal blocks and does not check that a
block kept its chromosome.
Super class
PolyGenius::Rule -> LiftoverLDBlocksRule
Methods
Public methods
LiftoverLDBlocksRule$new()LiftoverLDBlocksRule$matches()LiftoverLDBlocksRule$inputs()LiftoverLDBlocksRule$requirements()LiftoverLDBlocksRule$run()LiftoverLDBlocksRule$clone()
Method new()
Create the LD block boundary liftover rule.
Usage
LiftoverLDBlocksRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
LiftoverLDBlocksRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
Build dependency inputs: the liftover packages, the source build's block set, and the chain between the two builds.
Usage
LiftoverLDBlocksRule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list of dependency specs.
Method requirements()
Declare runtime requirements.
Usage
LiftoverLDBlocksRule$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 block set and store the canonical partition.
Usage
LiftoverLDBlocksRule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Bound input values from inputs().
logger — Rule-scoped logger.
Returns
Named list: data (path), meta, logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
LiftoverLDBlocksRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.