Commit c76e4146 authored by ziegenhain@bio.lmu.de's avatar ziegenhain@bio.lmu.de
Browse files

bugfix: prevent crash when downsampling is out of range

parent b1c534e0

barcodeIDFUN.R

+5 −0
Original line number Diff line number Diff line
@@ -14,6 +14,11 @@ setDownSamplingOption<-function( down ,bccount, filename=NULL){ 
      subn=as.numeric(down)

      subsample.splits <- matrix( c(subn,subn),1,2 )

    }

    if(any(subsample.splits[,1] > max(bccount$n))){

      print("Warning! None of the barcodes had enough reads for the following requested downsampling:")

      print(row.names(subsample.splits)[which(subsample.splits[,1] > max(bccount$n))])

      subsample.splits <- subsample.splits[which(subsample.splits[,1] <= max(bccount$n)),]

    }

  }else{

    mads<-calcMADS(bccount)

    plotReadCountSelection(bccount,mads,  filename=filename)

zUMIs-dge2.R

+6 −1
Original line number Diff line number Diff line
@@ -59,7 +59,12 @@ subS<-setDownSamplingOption( opt$counting_opts$downsampling, 
                             bccount= bccount,

                             filename=paste(opt$out_dir,"/zUMIs_output/stats/",opt$project,

                                            ".downsampling_thresholds.pdf",sep=""))



print("Here are the detected subsampling options:")

if(is.null(row.names(subS))){

  print("Automatic downsampling")

}else{

  print(row.names(subS))

}

if( opt$counting_opts$introns ){

  mapList<-list("exon"="exon",

                "inex"=c("intron","exon"),

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