Commit f4b0b185 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added excludeNonVariants

parent a26063f4
......@@ -21,6 +21,7 @@ class CombineVariants(val root: Configurable) extends Gatk {
var rodPriorityList: String = null
var minimumN: Int = config("minimumN", default = 1)
var genotypeMergeOptions: Option[String] = config("genotypeMergeOptions")
var excludeNonVariants: Boolean = false
var inputMap: Map[File, String] = Map()
......@@ -46,5 +47,6 @@ class CombineVariants(val root: Configurable) extends Gatk {
required("-o", outputFile) +
optional("--setKey", setKey) +
optional("--rod_priority_list", rodPriorityList) +
optional("-genotypeMergeOptions", genotypeMergeOptions)
optional("-genotypeMergeOptions", genotypeMergeOptions) +
conditional(excludeNonVariants, "--excludeNonVariants")
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment