Fixed type

e57304d0 · Peter van 't Hof · a508e6f8 · e57304d0
Commit e57304d0 authored Apr 27, 2016 by Peter van 't Hof
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala ...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala +1 -1

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--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
@@ -512,7 +512,7 @@ object HaplotypeCaller {
  def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
    val hc = apply(root, List(inputFile), outputFile)
    hc.emitRefConfidence = "GVCF"
-    hc.variant_index_type = GATKVCFIndexType.LINEAR
+    hc.variant_index_type = Some("LINEAR")
    hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
    hc
  }