Commit d50a9777 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix on config load

parent f4576dca
......@@ -7,13 +7,9 @@ class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.q
memoryLimit = Option(4)
override val defaultVmem = "8G"
override def afterGraph {
super.afterGraph
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").getString)
if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").getString)
}
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").getString)
if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").getString)
}
object BaseRecalibrator {
......
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