Commit b457ed22 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added index file as output file

parent 2a998e22
......@@ -26,11 +26,20 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
@Output(doc = "Output vcf file", shortName = "output", required = true)
var output: File = _
@Output(doc = "Output vcf file index", shortName = "output", required = true)
private var outputIndex: File = _
var reference: File = config("reference")
override val defaultVmem = "8G"
memoryLimit = Option(4)
override def afterGraph {
super.afterGraph
if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
}
override def commandLine = super.commandLine +
repeat("-I", input) +
required("-o", output) +
......
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