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Merged
LTLA merged 3 commits into from
Jun 19, 2025
Merged

Small code simplification #29

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1992e39
Small code simplification
hpages Jun 18, 2025
e6ebfb3
Merge remote-tracking branch 'upstream/master'
LTLA Jun 19, 2025
50be402
Bumped version and date.
LTLA Jun 19, 2025
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: TileDBArray
Version: 1.19.0
Date: 2024-10-01
Version: 1.19.1
Date: 2025-06-19
Title: Using TileDB as a DelayedArray Backend
Description: Implements a DelayedArray backend for reading and
writing dense or sparse arrays in the TileDB format. The
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3 changes: 1 addition & 2 deletions NAMESPACE
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Expand Up @@ -45,7 +45,6 @@ importFrom(S4Vectors,isSingleString)
importFrom(S4Vectors,setValidity2)
importFrom(SparseArray,COO_SparseArray)
importFrom(SparseArray,extract_sparse_array)
importFrom(SparseArray,nzcoo)
importFrom(SparseArray,nzdata)
importFrom(SparseArray,nzvals)
importFrom(SparseArray,nzwhich)
importFrom(methods,show)
12 changes: 3 additions & 9 deletions R/TileDBRealizationSink.R
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Expand Up @@ -207,22 +207,16 @@ setValidity2("TileDBRealizationSink", function(object) {

#' @export
#' @importClassesFrom SparseArray COO_SparseArray
#' @importFrom SparseArray nzcoo nzdata nzwhich
#' @importFrom SparseArray nzwhich nzvals
#' @importFrom DelayedArray start width
setMethod("write_block", "TileDBRealizationSink", function(sink, viewport, block) {
starts <- start(viewport) - 1L
obj <- tiledb_array(sink@path, attrs=sink@attr, query_type="WRITE")
on.exit(tiledb_array_close(obj))

if (sink@sparse) {
# Need this because COO_SparseArray doesn't support [.
if (is(block, "COO_SparseArray")) {
idx <- nzcoo(block)
vals <- nzdata(block)
} else {
idx <- nzwhich(block, arr.ind=TRUE)
vals <- block[idx]
}
idx <- nzwhich(block, arr.ind=TRUE)
vals <- nzvals(block)

ndim <- ncol(idx)
store <- vector("list", ndim + 1L)
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