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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4433 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-10-05 19:04:10 +00:00
parent e8af776b99
commit 28ac1d325e
1 changed files with 3 additions and 3 deletions
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4
scala/qscript/chartl/RefineGenotypesAndMerge.q
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@ -11,7 +11,7 @@ import collection.JavaConversions._
import org.broadinstitute.sting.utils.yaml.YamlUtils import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
class BeagleGenotypeRefinement extends QScript { class RefineGenotypesAndMerge extends QScript {
qscript => qscript =>
@Argument(doc="VCF file to run beagle genotype refinement on",required=true,shortName="vcf") var vcfsToBeagle: List[File] = _ @Argument(doc="VCF file to run beagle genotype refinement on",required=true,shortName="vcf") var vcfsToBeagle: List[File] = _
@ -95,7 +95,7 @@ class BeagleGenotypeRefinement extends QScript {
def mergeVCFs(vcfs: List[File], outputVCF: File) : CombineVariants = { def mergeVCFs(vcfs: List[File], outputVCF: File) : CombineVariants = {
var cv = new CombineVariants with GATKArgs var cv = new CombineVariants with GATKArgs
cv.out = outputVCF cv.out = outputVCF
cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY) cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED)
cv.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) cv.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
cv.priority = (vcfs.foldLeft[List[String]](Nil)( (bNames,vcf) => bNames ::: List[String](swapExt(vcf,".vcf","").getName))).mkString(",") cv.priority = (vcfs.foldLeft[List[String]](Nil)( (bNames,vcf) => bNames ::: List[String](swapExt(vcf,".vcf","").getName))).mkString(",")
cv.rodBind = vcfs.foldLeft[List[RodBind]](Nil)( (rods,vcf) => rods ::: List[RodBind](new RodBind(swapExt(vcf,".vcf","").getName,"VCF",vcf))) cv.rodBind = vcfs.foldLeft[List[RodBind]](Nil)( (rods,vcf) => rods ::: List[RodBind](new RodBind(swapExt(vcf,".vcf","").getName,"VCF",vcf)))