prevent crashing when wrong barcodefile is given (61010084) · Commits · github_fork / ZUMIs

barcodeIDFUN.R

+13 −1

Original line number	Diff line number	Diff line
		@@ -101,7 +101,19 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){
		}
		.cellBarcode_known <- function( bccount, bcfile ){
		bc<-read.table(bcfile,header = F,stringsAsFactors = F)$V1
		if( any( bc %in% bccount$XC ) ){
		bccount[XC %in% bc,keep:=TRUE]
		}else{
		print("Warning! None of the annotated barcodes were detected.")
		if(nrow(bccount)<100){
		print("Less than 100 barcodes present, will continue with all barcodes...")
		bccount[1:nrow(bccount),keep:=TRUE]
		}else{
		print("Continuing with top 100 barcodes instead...")
		bccount[1:100,keep:=TRUE]
		}
		}

		return(bccount[keep==TRUE,XC])
		}