Commit e274f59e authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed compile errors

parent 7abb542a
......@@ -5,46 +5,6 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
//import java.io.File
//
//import nl.lumc.sasc.biopet.utils.config.Configurable
//import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
//
//class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
//
// @Gather(enabled = false)
// @Output(required = false)
// protected var vcfIndex: File = _
//
// 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 val defaultThreads = 1
//
// override def freezeFieldValues() {
// super.freezeFieldValues()
//
// genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
// nct = Some(getThreads)
// memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
// }
//}
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -180,7 +140,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** The minimum phred-scaled confidence threshold at which variants should be called */
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false, exclusiveOf = "", validation = "")
var standard_min_confidence_threshold_for_calling: Option[Double] = config("standard_min_confidence_threshold_for_calling")
var standard_min_confidence_threshold_for_calling: Option[Double] = config("stand_call_conf")
/** Format string for standard_min_confidence_threshold_for_calling */
@Argument(fullName = "standard_min_confidence_threshold_for_callingFormat", shortName = "", doc = "Format string for standard_min_confidence_threshold_for_calling", required = false, exclusiveOf = "", validation = "")
......@@ -188,7 +148,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
/** The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold) */
@Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false, exclusiveOf = "", validation = "")
var standard_min_confidence_threshold_for_emitting: Option[Double] = config("standard_min_confidence_threshold_for_emitting")
var standard_min_confidence_threshold_for_emitting: Option[Double] = config("stand_emit_conf")
/** Format string for standard_min_confidence_threshold_for_emitting */
@Argument(fullName = "standard_min_confidence_threshold_for_emittingFormat", shortName = "", doc = "Format string for standard_min_confidence_threshold_for_emitting", required = false, exclusiveOf = "", validation = "")
......
......@@ -5,12 +5,10 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
//class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
//}
......@@ -80,7 +78,7 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
/** Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context */
@Argument(fullName = "sample", shortName = "sn", doc = "Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context", required = false, exclusiveOf = "", validation = "")
var sample: List[String] = config("sample", default = Nil, freeVar = false
var sample: List[String] = config("sample", default = Nil, freeVar = false)
/** Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets */
@Argument(fullName = "known_names", shortName = "knownName", doc = "Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets", required = false, exclusiveOf = "", validation = "")
......
......@@ -17,7 +17,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
def biopetScript() {
val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
ug.alleles = config("input_alleles")
ug.genotyping_mode = "GENOTYPE_GIVEN_ALLELES"
ug.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
add(ug)
}
}
......@@ -38,7 +38,8 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
override def defaults = Map(
"haplotypecaller" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0),
"genotypegvcfs" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0)
"genotypegvcfs" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0),
"unifiedgenotyper" -> Map("stand_call_conf" -> 30, "stand_emit_conf" -> 0)
)
/** Method to make the variantcalling namespace of shiva */
......
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