Commit 9b8e7dd8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix inspection warnings

parent 046d7d2b
......@@ -35,7 +35,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var inputVCF: File = _
def init(): Unit = {
}
override def defaults = ConfigUtils.mergeMaps(Map(
......@@ -63,28 +62,26 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var outputFile = normalizer.outputVcf
gonlVcfFile match {
case Some(gonlVcfFile) => {
case Some(gonlFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
vcfWithVcf.secondaryVcf = gonlVcfFile
vcfWithVcf.secondaryVcf = gonlFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
}
case _ =>
}
exacVcfFile match {
case Some(exacVcfFile) => {
case Some(exacFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
vcfWithVcf.secondaryVcf = exacVcfFile
vcfWithVcf.secondaryVcf = exacFile
vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
}
case _ =>
}
}
......
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