Commit e57304d0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed type

parent a508e6f8
...@@ -512,7 +512,7 @@ object HaplotypeCaller { ...@@ -512,7 +512,7 @@ object HaplotypeCaller {
def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = { def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
val hc = apply(root, List(inputFile), outputFile) val hc = apply(root, List(inputFile), outputFile)
hc.emitRefConfidence = "GVCF" 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.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
hc hc
} }
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