Commit afd60c92 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed region selectvariants

parent 1d64d452
......@@ -80,9 +80,13 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val chunkName = s"${region.chr}-${region.start}-${region.end}"
val chunkDir = new File(outputDir, "chunk" + File.separator + chunkName)
val bedFile = new File(chunkDir, chunkName + ".bed")
val sv = new SelectVariants(this)
sv.inputFiles :+= useVcf
sv.outputFile = new File(chunkDir, chunkName + ".vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
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