bug fix on filtering microexons

lingminhao · lingminhao · commit dbc3416293df · 2025-03-17T12:03:15.000+08:00
diff --git a/R/prepareDataFromBam.R b/R/prepareDataFromBam.R
@@ -95,7 +95,7 @@ prepareDataFromBam <- function(bamFile, yieldSize = NULL, verbose = FALSE,
         readGrgList <- readGrgList[[1]]
     }
     # remove microexons of width 1bp from list
-    readGrgList <- readGrgList[width(readGrgList) > 1]
+    readGrgList <- readGrgList <- readGrgList[sum(width(readGrgList)) > 1]
     numNoBCs <- sum(is.na(mcols(readGrgList)$BC))
     if(numNoBCs > 0){
         message("Removing ", numNoBCs, " reads that were not assigned barcodes. If this is unexpected check the barcode map input")

Original file line number	Diff line number	Diff line change
`@@ -95,7 +95,7 @@ prepareDataFromBam <- function(bamFile, yieldSize = NULL, verbose = FALSE,`
`95`	`95`	`readGrgList <- readGrgList[[1]]`
`96`	`96`	`}`
`97`	`97`	`# remove microexons of width 1bp from list`
`98`		`- readGrgList <- readGrgList[width(readGrgList) > 1]`
	`98`	`+ readGrgList <- readGrgList <- readGrgList[sum(width(readGrgList)) > 1]`
`99`	`99`	`numNoBCs <- sum(is.na(mcols(readGrgList)$BC))`
`100`	`100`	`if(numNoBCs > 0){`
`101`	`101`	`message("Removing ", numNoBCs, " reads that were not assigned barcodes. If this is unexpected check the barcode map input")`