Commit 175de69a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding error on missing alleles

parent dee3612b
......@@ -20,6 +20,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import nl.lumc.sasc.biopet.extensions.gatk
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
......@@ -27,9 +28,11 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
val name = "haplotypecaller_allele"
protected def defaultPrio = 5
val alleles: File = config("input_alleles")
def biopetScript() {
val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)
hc.alleles = config("input_alleles")
hc.alleles = Some(alleles)
hc.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
add(hc)
}
......
......@@ -27,9 +27,11 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
val name = "unifiedgenotyper_allele"
protected def defaultPrio = 9
val alleles: File = config("input_alleles")
def biopetScript() {
val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
ug.alleles = config("input_alleles")
ug.alleles = Some(alleles)
ug.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
add(ug)
}
......
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