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

Fix some options

parent b36e7c85
...@@ -9,36 +9,36 @@ import nl.lumc.sasc.biopet.core.config.Configurable ...@@ -9,36 +9,36 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral { class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
override def afterGraph { min_mapping_quality_score = config("minMappingQualityScore", default = 20)
super.afterGraph if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
min_mapping_quality_score = config("minMappingQualityScore", default = 20) this.sample_ploidy = config("ploidy")
if (config.contains("scattercount")) scatterCount = config("scattercount") nct = config("threads", default = 1)
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp") if (config.contains("bamOutput")) bamOutput = config("bamOutput")
this.sample_ploidy = config("ploidy") memoryLimit = Option(nct.getOrElse(1) * 2)
nct = config("threads", default = 1) if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
bamOutput = config("bamOutput") if (config.contains("output_mode")) {
memoryLimit = Option(nct.getOrElse(1) * 2) import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs") config("output_mode").asString match {
if (config.contains("output_mode")) { case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._ case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
config("output_mode").asString match { case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES case e => logger.warn("output mode '" + e + "' does not exist")
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") { if (config("inputtype", default = "dna").asString == "rna") {
dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true) dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
stand_call_conf = config("stand_call_conf", default = 5) stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0) stand_emit_conf = config("stand_emit_conf", default = 0)
} else { } else {
dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false) dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
stand_call_conf = config("stand_call_conf", default = 5) stand_call_conf = config("stand_call_conf", default = 5)
stand_emit_conf = config("stand_emit_conf", default = 0) stand_emit_conf = config("stand_emit_conf", default = 0)
} }
override def afterGraph {
super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) { if (bamOutput != null && nct.getOrElse(1) > 1) {
nct = Option(1) nct = Option(1)
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug") logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
......
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