DelayedArray back end for plink2 bed, before I learned about BEDMatrix

bedarray.R

library(DelayedArray)

setClass("plBedSeed",
  contains="Array",
  slots = c(
   dim = "integer",
   bedreaderRef = "ANY",
   dimnames = "list"
   )
)

plBedSeed = function(bedreaderRef) {
   dims = as.integer(unlist(bedreaderRef$shape))
   props = bedreaderRef$properties
   dimnames = list(seq_len(length(props$fid)), props$sid)
   new("plBedSeed", dim=dims, bedreaderRef=bedreaderRef, dimnames=dimnames)
}

setMethod("extract_array", c("plBedSeed"), function(x, index) {
   reticulate::py_require("numpy")
   np = reticulate::import("numpy")
   br = slot(x, "bedreaderRef")
   as.matrix(b3$read(np$s_[as.integer(index[[2]]-1)])[index[[1]],,drop=FALSE])
})


setClass("plBedArray", contains="DelayedArray", representation(seed="plBedSeed"))

plBedArray = function(bedreaderRef)
   DelayedArray(plBedSeed(bedreaderRef))