remove lowMemory which causes the error when specifying readClass.outputDir

Author: SuiYue-2308

R/bambu-processReads.R

@@ -106,16 +106,12 @@ bambu.processReads <- function(reads, annotations, genomeSequence,
     if (!is.null(readClass.outputDir)) {
         for(i in seq_along(readClassList)){
             readClassFile <- "combinedSamples"
-            if(lowMemory){
-                readClassFile <- metadata(readClassList[[i]])$sampleNames
-            }
             readClassFile <- BiocFileCache::bfcnew(BiocFileCache::BiocFileCache(
                 readClass.outputDir, ask = FALSE),
                 paste0(readClassFile,"_readClassSe"), ext = ".rds")
             saveRDS(readClassList[[i]], file = readClassFile)
             readClassList[[i]] <- readClassFile
         }
-        
     }
     #TODO don't output list, current there because discovery needs it
     return(readClassList)

R/bambu.R

@@ -138,7 +138,7 @@
 bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
     mode = NULL, opt.discovery = NULL, opt.em = NULL, rcOutDir = NULL, discovery = TRUE, 
     assignDist = TRUE, quant = TRUE, stranded = FALSE,  ncore = 1, yieldSize = NULL,  
-    trackReads = FALSE, returnDistTable = FALSE, lowMemory = FALSE, 
+    trackReads = FALSE, returnDistTable = FALSE,
     fusionMode = FALSE, verbose = FALSE, demultiplexed = FALSE, spatial = NULL, quantData = NULL,
     sampleNames = NULL, cleanReads = FALSE, dedupUMI = FALSE, barcodesToFilter = NULL, clusters = NULL,
     processByChromosome = FALSE, processByBam = TRUE) {
@@ -165,9 +165,6 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
             returnDistTable <- TRUE
         }
     }
-    if(lowMemory)
-        message("lowMemory has been deprecated and split into processByChromosome and processByBam. Please see Documentation")
-    
     if(is.null(annotations)){ 
         annotations <- GRangesList()
     } else {