diff --git a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala index 77ebb3d08..4829e7a02 100644 --- a/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala +++ b/scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala @@ -11,16 +11,40 @@ import java.text.SimpleDateFormat import java.util.Date class FullCallingPipelineTest extends BaseTest { - def datasets = List(k1gChr20Dataset) + def datasets = List(k1gChr20Dataset, k1gExomeDataset) private final val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/" val k1gChr20Dataset = { + val dataset = newK1gDataset + dataset.pipeline.getProject.setName("Barcoded_1000G_WEx_chr20") + dataset.pipeline.getProject.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list")) + + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "1390", "1420") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.52", "3.60") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.71", "3.80") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.79", "2.86") + + dataset + } + + val k1gExomeDataset = { + val dataset = newK1gDataset + dataset.pipeline.getProject.setName("Barcoded_1000G_WEx") + dataset.pipeline.getProject.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list")) + + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "51969", "53019") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.18", "3.25") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.29", "3.36") + dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.80", "2.87") + + dataset + } + + def newK1gDataset = { val project = new PipelineProject - project.setName("Barcoded_1000G_WEx_chr20") project.setReferenceFile(new File(BaseTest.hg19Reference)) project.setDbsnpFile(new File(BaseTest.b37dbSNP129)) - project.setIntervalList(new File(BaseTest.GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list")) val squid = "C426" val ids = List( @@ -43,12 +67,6 @@ class FullCallingPipelineTest extends BaseTest { dataset.pipeline = pipeline dataset.refseq = BaseTest.hg19Refseq dataset.targetTiTv = "3.0" - dataset.jobQueue = "hour" - - dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.counter.nCalledLoci", "1390", "1420") - dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.all.titv.tiTvRatio", "3.52", "3.60") - dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.known.titv.tiTvRatio", "3.71", "3.80") - dataset.validations :+= new PipelineValidation("evalHandFiltered.dbsnp.all.called.novel.titv.tiTvRatio", "2.79", "2.86") dataset } @@ -84,7 +102,7 @@ class FullCallingPipelineTest extends BaseTest { val optimizedVcf = PipelineTest.runDir(testName) + "SnpCalls/%s.uncleaned.annotated.indel.masked.recalibrated.tranched.vcf".format(projectName) // eval modules to record in the validation directory - val evalModules = List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator") + val evalModules = List("CompOverlap", "CountFunctionalClasses", "CountVariants", "SimpleMetricsBySample", "TiTvVariantEvaluator") // write the report to the shared validation data location val formatter = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss")