Commit 833cf3c1 authored by Sander Bollen's avatar Sander Bollen
Browse files

add the options in the list

parent 8b471bb1
......@@ -39,6 +39,20 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
var minSamplesPass: Option[Int] = config("min_samples_pass")
var minGenomeQuality: Option[Int] = config("min_genome_quality")
var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
var invertedOutputVcf: Option[File] = None
var resToDom: Option[String] = None
var trioCompound: Option[String] = None
var deNovoInSample: Option[String] = None
var deNovoTrio: Option[String] = None
var trioLossOfHet: Option[String] = None
var mustHaveVariant: List[String] = Nil
var calledIn: List[String] = Nil
var mustHaveGenotype: List[String] = Nil
var diffGenotype: List[String] = Nil
var filterHetVarToHomVar: List[String] = Nil
var minQualScore: Option[Double] = None
var id: List[String] = Nil
var idFile: Option[File] = None
override def defaultCoreMemory = 3.0
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