Commit 4bd9f01e authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing type warnings

parent 3a2bb70d
......@@ -39,14 +39,16 @@ class Impute2Vcf(val root: Configurable) extends QScript with BiopetQScript with
val phenotypeFile: File = config("phenotype_file")
val inputGens: List[GensInput] = config("input_gens", default = Nil).asList.map {
case value: Map[String, Any] =>
GensInput(new File(value("genotypes").toString),
value.get("info").map(x => new File(x.toString)),
value("contig").toString)
case value: util.LinkedHashMap[String, _] =>
GensInput(new File(value.get("genotypes").toString),
value.toMap.get("info").map(x => new File(x.toString)),
value.get("contig").toString)
case value: Map[_, _] =>
val map = value.map(x => x._1.toString -> x._2)
GensInput(new File(map("genotypes").toString),
map.get("info").map(x => new File(x.toString)),
map("contig").toString)
case value: util.LinkedHashMap[_, _] =>
val map = value.map(x => x._1.toString -> x._2)
GensInput(new File(map("genotypes").toString),
map.get("info").map(x => new File(x.toString)),
map("contig").toString)
case _ => throw new IllegalArgumentException
} ++ (specsFile match {
case Some(file) => Impute2Vcf.imputeSpecsToGensInput(file, config("validate_specs", default = true))
......
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