tidy for cleaner code

Author: lingminhao

R/bambu-processReads.R

@@ -54,7 +54,7 @@ bambu.processReads <- function(reads, annotations, genomeSequence,
     returnModel <- isoreParameters[["returnModel"]]
     min.exonOverlap <- isoreParameters[["min.exonOverlap"]]
 
-    if(processByBam){ # bulk mode
+    if(processByBam){
         readClassList <- bplapply(seq_along(reads), function(i) {
             bambu.processReadsByFile(bam.file = reads[i],
             genomeSequence = genomeSequence,annotations = annotations,
@@ -64,7 +64,7 @@ bambu.processReads <- function(reads, annotations, genomeSequence,
             processByChromosome = processByChromosome, trackReads = trackReads, fusionMode = fusionMode, 
             demultiplexed = demultiplexed, cleanReads = cleanReads, dedupUMI = dedupUMI, index = 1, barcodesToFilter = barcodesToFilter)},
             BPPARAM = bpParameters)
-    } else { # single cell mode 
+    } else {
         readGrgList <- bplapply(seq_along(reads), function(i) {
             bambu.readsByFile(bam.file = reads[i],
             genomeSequence = genomeSequence,annotations = annotations,
@@ -173,10 +173,7 @@ bambu.processReadsByFile <- function(bam.file, genomeSequence, annotations,
 
     mcols(readGrgList)$id <- seq_along(readGrgList) 
 
-    sampleName <- names(bam.file)[1]
-
     if(!isFALSE(demultiplexed)){ 
-        mcols(readGrgList)$CB <- as.factor(mcols(readGrgList)$CB)
         mcols(readGrgList)$sampleID <- as.numeric(mcols(readGrgList)$CB)
     } else {
         mcols(readGrgList)$sampleID <- index
@@ -409,7 +406,7 @@ splitReadClassFiles = function(readClassFile){
         i = rep(seq_along(counts.table), lengths(counts.table)),
         j = as.numeric(names(unlist(counts.table))),
         x = unlist(counts.table),
-        dims = c(nrow(eqClasses), length(metadata(readClassFile)$sampleData$id)))
+        dims = c(nrow(eqClasses), nrow(metadata(readClassFile)$sampleData)))
     #incompatible counts
     distTable <- metadata(metadata(readClassFile)$readClassDist)$distTable.incompatible
     if(nrow(distTable)==0) {

R/bambu_utilityFunctions.R

@@ -310,14 +310,14 @@ generateColData <- function(readClassList, sampleMetadata, demultiplexed) {
 
   joinKey <- if (demultiplexed) "barcode" else "sampleName"
 
+  colData <- tibble(
+      id = metadata(readClassList)$sampleData$id, 
+      sampleName = metadata(readClassList)$sampleData$sampleName
+  ) 
+
   if (demultiplexed) {
-    colData <- tibble(
-        id = paste(metadata(readClassList)$sampleData$sampleName, metadata(readClassList)$sampleData$barcode, sep = '_'),
-        sampleName = metadata(readClassList)$sampleData$sampleName,
-        barcode = metadata(readClassList)$sampleData$barcode
-    )
-  } else{
-    colData <- tibble(id = metadata(readClassList)$sampleData$sampleName, sampleName = metadata(readClassList)$sampleData$sampleName)
+      colData <- colData %>%
+        mutate(barcode = metadata(readClassList)$sampleData$barcode)
   }
 
   colData <- colData %>%

R/prepareDataFromBam.R

@@ -101,6 +101,11 @@ prepareDataFromBam <- function(bamFile, yieldSize = NULL, verbose = FALSE,
     } else {
         readGrgList <- readGrgList[[1]]
     }
+
+    if (demultiplexed){
+        mcols(readGrgList)$CB <- as.factor(mcols(readGrgList)$CB)
+    }
+
     # remove microexons of width 1bp from list
     readGrgList <- readGrgList <- readGrgList[sum(width(readGrgList)) > 1]
     numNoCBs <- sum(is.na(mcols(readGrgList)$CB))