Commit 7a573705 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix scattercounts

parent 46cef440
......@@ -8,32 +8,29 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.config.Configurable
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
sample_ploidy = config("ploidy")
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0)
if (config.contains("output_mode")) {
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config("output_mode").asString 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")
}
}
override def beforeGraph {
super.beforeGraph
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
nct = Some(getThreads(1))
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").asString 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").asString == "rna") {
stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0)
} else {
stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0)
}
memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
}
}
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