From 28ac1d325eb3660e8779a9eeb94f6fd441e69e95 Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 5 Oct 2010 19:04:10 +0000 Subject: [PATCH] Commit for Ryan git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4433 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/chartl/RefineGenotypesAndMerge.q | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scala/qscript/chartl/RefineGenotypesAndMerge.q b/scala/qscript/chartl/RefineGenotypesAndMerge.q index ff6593e9a..d7c747b5f 100755 --- a/scala/qscript/chartl/RefineGenotypesAndMerge.q +++ b/scala/qscript/chartl/RefineGenotypesAndMerge.q @@ -11,7 +11,7 @@ import collection.JavaConversions._ import org.broadinstitute.sting.utils.yaml.YamlUtils import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType -class BeagleGenotypeRefinement extends QScript { +class RefineGenotypesAndMerge extends QScript { qscript => @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 = { var cv = new CombineVariants with GATKArgs 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.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))) @@ -116,4 +116,4 @@ class BeagleGenotypeRefinement extends QScript { add(mergeVCFs(vcfsToMerge,outVCF)) } -} \ No newline at end of file +}