From 6ca4e3cebfa5ce337c81fef06da0d253182241e3 Mon Sep 17 00:00:00 2001 From: kshakir Date: Mon, 25 Apr 2011 21:37:04 +0000 Subject: [PATCH] Updating FCPT nCalledLoci due to fixed QD<2.0 filter. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5686 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/FullCallingPipelineTest.scala | 23 ++++--------------- 1 file changed, 4 insertions(+), 19 deletions(-) diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala index 42d1144ee..ed7558472 100644 --- a/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala +++ b/scala/test/org/broadinstitute/sting/queue/pipeline/playground/FullCallingPipelineTest.scala @@ -32,14 +32,14 @@ import org.broadinstitute.sting.utils.yaml.YamlUtils import org.broadinstitute.sting.queue.pipeline._ class FullCallingPipelineTest { - def datasets = List(k1gChr20Dataset)//, k1gExomeDataset) + def datasets = List(k1gChr20Dataset) val k1gChr20Dataset = { val dataset = newK1gDataset("Barcoded_1000G_WEx_chr20", true) - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 1398) - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 1143) - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 255) + dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 1391) + dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 1142) + dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 249) dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.all", "tiTvRatio", 3.6250) dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.known", "tiTvRatio", 3.7190) dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.novel", "tiTvRatio", 3.2037) @@ -47,21 +47,6 @@ class FullCallingPipelineTest { dataset } - val k1gExomeDataset = { - val dataset = newK1gDataset("Barcoded_1000G_WEx", false) - - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.all", "nCalledLoci", 52668) - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.known", "nCalledLoci", 41248) - dataset.validations :+= new IntegerValidation("CountVariants", "dbsnp.eval.novel", "nCalledLoci", 11420) - dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.all", "tiTvRatio", 3.271) - dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.known", "tiTvRatio", 3.3299) - dataset.validations :+= new DoubleValidation("TiTvVariantEvaluator", "dbsnp.eval.novel", "tiTvRatio", 3.0487) - - dataset.jobQueue = "gsa" - - dataset - } - def newK1gDataset(projectName: String, chr20: Boolean) = { val project = PipelineTest.createHg19Project(projectName, chr20) var samples = List.empty[PipelineSample]