Commit c008141f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix some options

parent b36e7c85
......@@ -9,15 +9,12 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
override def afterGraph {
super.afterGraph
min_mapping_quality_score = config("minMappingQualityScore", default = 20)
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
nct = config("threads", default = 1)
bamOutput = config("bamOutput")
if (config.contains("bamOutput")) bamOutput = config("bamOutput")
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
......@@ -39,6 +36,9 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0)
}
override def afterGraph {
super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
nct = Option(1)
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
......
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