Commit b9f88a39 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Minor code refactor

parent 4842dd5c
......@@ -10,13 +10,11 @@ import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
min_mapping_quality_score = config("minMappingQualityScore", default = 20)
if (config.contains("scattercount")) scatterCount = config("scattercount")
scatterCount = config("scattercount", default = 1)
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
nct = config("threads", default = 1)
if (config.contains("bamOutput")) bamOutput = config("bamOutput")
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("allSitePLs")) allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config("output_mode").asString match {
......@@ -40,9 +38,11 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
override def afterGraph {
super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
nct = Option(1)
threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
nct = Some(threads)
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
def useGvcf() {
......
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