Commit 862aefe3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove obselete apply methods

parent 1062e3ab
......@@ -46,12 +46,6 @@ object BiopetFlagstat extends ToolCommand {
flagstat.output = output
return flagstat
def apply(root: Configurable, input: File, outputDir: String): BiopetFlagstat = {
val flagstat = new BiopetFlagstat(root)
flagstat.input = input
flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
return flagstat
case class Args(inputFile: File = null, region: Option[String] = None) extends AbstractArgs
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