Commit 8d17bcbb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Add output_mode option

parent a5616824
......@@ -14,6 +14,15 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
bamOutput = config("bamOutput")
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")){
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config("output_mode").getString match {
case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
case e => logger.warn("output mode '" + e + "' does not exist")
}
}
if (config("inputtype", default = "dna").getString == "rna") {
dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
......
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