Commit 95f8441a authored by Peter van 't Hof's avatar Peter van 't Hof

fixed a config value

parent bfdad518
......@@ -90,7 +90,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** Mode for emitting reference confidence scores */
@Argument(fullName = "emitRefConfidence", shortName = "ERC", doc = "Mode for emitting reference confidence scores", required = false, exclusiveOf = "", validation = "")
var emitRefConfidence: String = _
var emitRefConfidence: Option[String] = config("emitRefConfidence")
/** File to which assembled haplotypes should be written */
@Output(fullName = "bamOutput", shortName = "bamout", doc = "File to which assembled haplotypes should be written", required = false, exclusiveOf = "", validation = "")
......@@ -525,7 +525,7 @@ object HaplotypeCaller {
def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
val hc = apply(root, List(inputFile), outputFile)
hc.emitRefConfidence = "GVCF"
hc.emitRefConfidence = Some("GVCF")
hc.variant_index_type = Some("LINEAR")
hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
hc
......
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