refactor: remove bambu.spatial wrapper

Author: ch99l

NAMESPACE

@@ -2,7 +2,6 @@
 
 export(bambu)
 export(bambu.singlecell)
-export(bambu.spatial)
 export(plotBambu)
 export(prepareAnnotations)
 export(readFromGTF)

R/bambu.R

@@ -355,40 +355,3 @@ bambu.singlecell <- function(reads, annotations = NULL, genome = NULL, NDR = NUL
         quantData = quantData, dedupUMI = dedupUMI, clusters = clusters,
         processByChromosome = processByChromosome, processByBam = processByBam)
 }
-
-#' Spatial wrapper for bambu
-#' @title Spatial isoform reconstruction and quantification
-#' @description Wrapper around \code{\link{bambu}} for spatial transcriptomics
-#' data. Accepts an \code{opt.spatial} list for spatial specific parameters
-#' and passes all other arguments directly to \code{\link{bambu}}.
-#' @param opt.spatial A list of spatial specific parameters:
-#' \describe{
-#'     \item{extractBarcodeUMI}{Logical, whether to extract spot barcodes and
-#'     UMIs from BAM tags or read names. Defaults to FALSE}
-#'     \item{dedupUMI}{Logical, whether to perform UMI-based deduplication per
-#'     barcode. Defaults to FALSE}
-#'     \item{clusters}{A named list mapping cluster names to barcode vectors,
-#'     used for cluster-level transcript discovery. Defaults to NULL}
-#' }
-#' @inheritParams bambu
-#' @export
-bambu.spatial <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
-    mode = NULL, opt.discovery = NULL, opt.em = NULL, opt.spatial = NULL,
-    rcOutDir = NULL, discovery = TRUE, assignDist = TRUE, quant = TRUE,
-    stranded = FALSE, ncore = 1, yieldSize = NULL, trackReads = FALSE,
-    returnDistTable = FALSE, lowMemory = FALSE, sampleData = NULL,
-    fusionMode = FALSE, verbose = FALSE, quantData = NULL,
-    processByChromosome = FALSE, processByBam = TRUE) {
-    extractBarcodeUMI <- isTRUE(opt.spatial$extractBarcodeUMI)
-    dedupUMI <- isTRUE(opt.spatial$dedupUMI)
-    clusters <- opt.spatial$clusters
-    bambu(reads = reads, annotations = annotations, genome = genome, NDR = NDR,
-        mode = mode, opt.discovery = opt.discovery, opt.em = opt.em,
-        rcOutDir = rcOutDir, discovery = discovery, assignDist = assignDist,
-        quant = quant, stranded = stranded, ncore = ncore, yieldSize = yieldSize,
-        trackReads = trackReads, returnDistTable = returnDistTable,
-        lowMemory = lowMemory, sampleData = sampleData, fusionMode = fusionMode,
-        verbose = verbose, extractBarcodeUMI = extractBarcodeUMI,
-        quantData = quantData, dedupUMI = dedupUMI, clusters = clusters,
-        processByChromosome = processByChromosome, processByBam = processByBam)
-}