Merge pull request #470 from GoekeLab/singleExon_2

remove the lowMemory and update example code for generating rcf

Author: Sui Yue

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, lowMemory = 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) {
@@ -167,7 +167,6 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
     }
     if(lowMemory)
         message("lowMemory has been deprecated and split into processByChromosome and processByBam. Please see Documentation")
-    
     if(is.null(annotations)){ 
         annotations <- GRangesList()
     } else {

README.md

@@ -352,7 +352,7 @@ se <- bambu(reads = info$rpath[1], annotations = annotations, genome = fa.file)
 
 This output is also generated when both quant and discovery are set to false in a list form indexed by sample.
 ```rscript
-se <- bambu(reads = test.bam, annotations = annotations, genome = fa.file, discovery = FALSE, quant = FALSE)
+se <- bambu(reads = test.bam, annotations = annotations, genome = fa.file, discovery = FALSE, quant = FALSE, assignDist = FALSE)
 ```
 
 As this is an intermediate object it will not be suitable to use for general use cases. We will document the object below for any potential advanced use cases that may arise.