From 6c99dc4dab0c6d352715e7bf75928f061769fc2f Mon Sep 17 00:00:00 2001 From: fromer Date: Mon, 31 Jan 2011 21:49:41 +0000 Subject: [PATCH] Take (partial) ownership of phasing 1000G chr20 calls git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5147 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/{depristo => fromer}/phaseSamples.scala | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) rename scala/qscript/oneoffs/{depristo => fromer}/phaseSamples.scala (96%) diff --git a/scala/qscript/oneoffs/depristo/phaseSamples.scala b/scala/qscript/oneoffs/fromer/phaseSamples.scala similarity index 96% rename from scala/qscript/oneoffs/depristo/phaseSamples.scala rename to scala/qscript/oneoffs/fromer/phaseSamples.scala index d0def5f22..fddfb392e 100644 --- a/scala/qscript/oneoffs/depristo/phaseSamples.scala +++ b/scala/qscript/oneoffs/fromer/phaseSamples.scala @@ -117,9 +117,7 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin this.rodBind :+= RodBind(vcf.getName, "VCF", vcf) } - // add the master call - this.rodBind :+= RodBind("master", "VCF", masterCalls) - this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER) + this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) this.out = new File("phased.vcf") }