Liftover backend backed by CrossMap

Liftover backend that shells out to the external CrossMap tool (CrossMap bed). CrossMap must be installed and on the PATH. For most interval workflows the R-native liftover_rtracklayer() backend is sufficient and easier to deploy; CrossMap is most valuable for allele-aware variant translation (see liftover_vcf()).

Usage

liftover_crossmap(intervals, chain, crossmap = NULL, ...)

Arguments

intervals

A tibble of intervals (see liftover_rtracklayer()).

chain

Path to a chain file.

crossmap

Path or name of the CrossMap executable. Defaults to auto-detection on the PATH.

...

Unused.

Value

A list with mapped and unmapped tibbles.

See also

liftover_intervals(), liftover_rtracklayer(), liftover_vcf()

Examples

if (nzchar(Sys.which("CrossMap")) || nzchar(Sys.which("CrossMap.py"))) {
  chain <- tempfile(fileext = ".chain")
  writeLines(
    c(
      "chain 1000 chr1 100000 + 0 1000 chrT 200000 + 10000 11000 1",
      "1000",
      ""
    ),
    chain
  )
  ints <- tibble::tibble(
    seqnames = c("chr1", "chr1"),
    start = c(100, 5000),
    end = c(200, 5100),
    .feature_id = 1:2
  )
  out <- liftover_crossmap(ints, chain)
  out$mapped
  unlink(chain)
}