Fixed config values

1b6fca2c · Peter van 't Hof · e66c1eec · 1b6fca2c
Commit 1b6fca2c authored Apr 18, 2017 by Peter van 't Hof
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
@@ -39,8 +39,8 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {

  val genderAwareCalling: Boolean = config("gender_aware_calling", default = false)
  val haploidRegions: Option[File] = config("hap̦loid_regions")
-  val haploidRegionsMale: Option[File] = config("haploid_regions")
-  val haploidRegionsFemale: Option[File] = config("haploid_regions")
+  val haploidRegionsMale: Option[File] = config("haploid_regions_male")
+  val haploidRegionsFemale: Option[File] = config("haploid_regions_female")

  lazy val refernceSize = referenceDict.getReferenceLength