tabixChrApply

Runs a function on reads/fragments from each chromosomes of a Tabix-indexed fragment file. This is especially used by other functions to avoid loading all alignments into memory, or to parallelize reads processing.

Usage

tabixChrApply(
  x,
  fn,
  keepSeqLvls = NULL,
  exclude = NULL,
  only = NULL,
  BPPARAM = SerialParam(),
  ...
)

Arguments

x

The path to a tabix-indexed bam file, or a TabixFile object.

fn

The function to be run, the first argument of which should be a `GRanges`

keepSeqLvls

An optional vector of seqLevels to keep

only

BPPARAM

A `BiocParallel` parameter object for multithreading. Note that if used, memory usage will be high; in this context we recommend a high `nChunks`.

...

Passed to `fn`

Value

A list of whatever `fn` returns