Commit b4acd8fd authored by bow's avatar bow
Browse files

Merge branch 'patch-genotyper' into 'develop'

Patch genotyper

Fix a small bug on unified genotyper

See merge request !125
parents 46cef440 7a573705
......@@ -8,16 +8,14 @@ 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 {
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)
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 {
......@@ -28,12 +26,11 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
}
}
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)
}
override def beforeGraph {
super.beforeGraph
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
nct = Some(getThreads(1))
memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
}
}
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