Test Summary

2223

tests
35

failures
0

ignored
24m32.11s

duration
98%

successful

Failed tests

Packages

Package Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender 11 0 0 2.119s 100%
org.broadinstitute.hellbender.cmdline 7 0 0 0.332s 100%
org.broadinstitute.hellbender.engine 117 1 0 1m39.01s 99%
org.broadinstitute.hellbender.engine.filters.flow 2 0 0 0.363s 100%
org.broadinstitute.hellbender.engine.spark 1 0 0 0.070s 100%
org.broadinstitute.hellbender.tools 364 0 0 2m56.26s 100%
org.broadinstitute.hellbender.tools.copynumber 184 0 0 1m4.90s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting 20 0 0 1.325s 100%
org.broadinstitute.hellbender.tools.copynumber.utils 23 0 0 1.570s 100%
org.broadinstitute.hellbender.tools.dragstr 15 0 0 2m59.18s 100%
org.broadinstitute.hellbender.tools.examples 30 0 0 7.034s 100%
org.broadinstitute.hellbender.tools.funcotator 82 0 0 1m58.87s 100%
org.broadinstitute.hellbender.tools.reference 39 0 0 2.963s 100%
org.broadinstitute.hellbender.tools.spark 67 0 0 1m18.22s 100%
org.broadinstitute.hellbender.tools.spark.bwa 3 0 0 2.480s 100%
org.broadinstitute.hellbender.tools.spark.pathseq 30 0 0 19.801s 100%
org.broadinstitute.hellbender.tools.spark.pipelines 337 34 0 1m49.29s 89%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics 22 0 0 3.040s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration 12 0 0 36.767s 100%
org.broadinstitute.hellbender.tools.spark.validation 6 0 0 3.378s 100%
org.broadinstitute.hellbender.tools.sv 25 0 0 1.280s 100%
org.broadinstitute.hellbender.tools.validation 6 0 0 0.626s 100%
org.broadinstitute.hellbender.tools.walkers 199 0 0 1m17.34s 100%
org.broadinstitute.hellbender.tools.walkers.annotator 34 0 0 18.448s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr 52 0 0 1m58.36s 100%
org.broadinstitute.hellbender.tools.walkers.consensus 2 0 0 0.822s 100%
org.broadinstitute.hellbender.tools.walkers.contamination 15 0 0 11.022s 100%
org.broadinstitute.hellbender.tools.walkers.conversion 9 0 0 0.752s 100%
org.broadinstitute.hellbender.tools.walkers.coverage 8 0 0 40.379s 100%
org.broadinstitute.hellbender.tools.walkers.fasta 28 0 0 2.047s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping 13 0 0 57.644s 100%
org.broadinstitute.hellbender.tools.walkers.filters 30 0 0 2.263s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth 14 0 0 10.608s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller 3 0 0 2.178s 100%
org.broadinstitute.hellbender.tools.walkers.mutect 2 0 0 5.769s 100%
org.broadinstitute.hellbender.tools.walkers.qc 13 0 0 1.104s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation 7 0 0 38.585s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter 1 0 0 2.354s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq 32 0 0 31.980s 100%
org.broadinstitute.hellbender.tools.walkers.sv 38 0 0 36.033s 100%
org.broadinstitute.hellbender.tools.walkers.validation 31 0 0 3.022s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup 2 0 0 0.812s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval 45 0 0 16.650s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling 2 0 0 0.960s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils 195 0 0 27.603s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr 27 0 0 38.854s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable 9 0 0 1.114s 100%
org.broadinstitute.hellbender.utils.config 3 0 0 0.447s 100%
org.broadinstitute.hellbender.utils.help 4 0 0 15.872s 100%
org.broadinstitute.hellbender.utils.python 1 0 0 0.153s 100%
org.broadinstitute.hellbender.utils.read 1 0 0 0.068s 100%

Classes

Class Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender.BwaMemIntegrationTest 2 0 0 0.233s 100%
org.broadinstitute.hellbender.IntelInflaterDeflaterIntegrationTest 6 0 0 1.572s 100%
org.broadinstitute.hellbender.PrintFileDiagnosticsIntegrationTest 3 0 0 0.314s 100%
org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidatorIntegrationTest 2 0 0 0.161s 100%
org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest 3 0 0 0.033s 100%
org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutorIntegrationTest 2 0 0 0.138s 100%
org.broadinstitute.hellbender.engine.BundleSupportIntegrationTest 1 0 0 0.008s 100%
org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest 45 0 0 1m17.56s 100%
org.broadinstitute.hellbender.engine.FeatureSupportIntegrationTest 6 0 0 0.483s 100%
org.broadinstitute.hellbender.engine.GatkToolIntegrationTest 22 0 0 1.582s 100%
org.broadinstitute.hellbender.engine.GenomicsDBIntegrationTest 7 0 0 1.636s 100%
org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest 17 1 0 10.461s 94%
org.broadinstitute.hellbender.engine.PartialReadWalkerIntegrationTest 2 0 0 0.068s 100%
org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest 1 0 0 3.293s 100%
org.broadinstitute.hellbender.engine.ReadWalkerIntegrationTest 2 0 0 0.134s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationSparkIntegrationTest 3 0 0 3.074s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationWalkerIntegrationTest 3 0 0 0.261s 100%
org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest 7 0 0 0.325s 100%
org.broadinstitute.hellbender.engine.WalkerOutputIntegrationTest 1 0 0 0.118s 100%
org.broadinstitute.hellbender.engine.filters.flow.WellFormedFlowBasedReadFilterIntegrationTest 2 0 0 0.363s 100%
org.broadinstitute.hellbender.engine.spark.GATKSparkToolIntegrationTest 1 0 0 0.070s 100%
org.broadinstitute.hellbender.tools.AddOriginalAlignmentTagsIntegrationTest 2 0 0 0.239s 100%
org.broadinstitute.hellbender.tools.BwaMemIndexImageCreatorIntegrationTest 1 0 0 2m17.47s 100%
org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotationsIntegrationTest 2 0 0 0.142s 100%
org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest 17 0 0 1.451s 100%
org.broadinstitute.hellbender.tools.CompareIntervalListsIntegrationTest 10 0 0 0.608s 100%
org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBamIntegrationTest 1 0 0 0.060s 100%
org.broadinstitute.hellbender.tools.CountBasesIntegrationTest 6 0 0 0.367s 100%
org.broadinstitute.hellbender.tools.CountReadsIntegrationTest 38 0 0 2.469s 100%
org.broadinstitute.hellbender.tools.CountVariantsIntegrationTest 10 0 0 7.332s 100%
org.broadinstitute.hellbender.tools.CreateBundleIntegrationTest 31 0 0 2.001s 100%
org.broadinstitute.hellbender.tools.DumpTabixIndexIntegrationTest 1 0 0 0.073s 100%
org.broadinstitute.hellbender.tools.FlagStatIntegrationTest 6 0 0 0.281s 100%
org.broadinstitute.hellbender.tools.GatherVcfsCloudIntegrationTest 12 0 0 0.994s 100%
org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest 3 0 0 0.218s 100%
org.broadinstitute.hellbender.tools.HtsgetReaderIntegrationTest 3 0 0 2.090s 100%
org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest 25 0 0 1.954s 100%
org.broadinstitute.hellbender.tools.LeftAlignIndelsIntegrationTest 1 0 0 0.192s 100%
org.broadinstitute.hellbender.tools.PrintBGZFBlockInformationIntegrationTest 8 0 0 0.519s 100%
org.broadinstitute.hellbender.tools.PrintReadsHeaderIntegrationTest 1 0 0 0.061s 100%
org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest 149 0 0 13.857s 100%
org.broadinstitute.hellbender.tools.SplitCRAMIntegrationTest 2 0 0 0.067s 100%
org.broadinstitute.hellbender.tools.SplitReadsIntegrationTest 35 0 0 3.820s 100%
org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervalsIntegrationTest 9 0 0 0.750s 100%
org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegmentsIntegrationTest 1 0 0 0.085s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsIntegrationTest 4 0 0 0.348s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest 4 0 0 2.470s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectReadCountsIntegrationTest 6 0 0 0.524s 100%
org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormalsIntegrationTest 36 0 0 10.300s 100%
org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest 48 0 0 2.976s 100%
org.broadinstitute.hellbender.tools.copynumber.FilterIntervalsIntegrationTest 30 0 0 2.106s 100%
org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCallerIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.copynumber.ModelSegmentsIntegrationTest 33 0 0 44.227s 100%
org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervalsIntegrationTest 12 0 0 1.113s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatiosIntegrationTest 7 0 0 0.474s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegmentsIntegrationTest 13 0 0 0.851s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpointsIntegrationTest 15 0 0 1.036s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotationIntegrationTest 1 0 0 0.068s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsIntegrationTest 2 0 0 0.129s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEventsIntegrationTest 5 0 0 0.337s 100%
org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModelIntegrationTest 12 0 0 1m51.32s 100%
org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFileIntegrationTest 3 0 0 1m7.86s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerIntegrationTest 1 0 0 0.994s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest 2 0 0 2.881s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectMultiMetricsIntegrationTest 2 0 0 0.606s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectSingleMetricsIntegrationTest 1 0 0 0.196s 100%
org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalkerIntegrationTest 2 0 0 0.139s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSparkIntegrationTest 1 0 0 0.387s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerIntegrationTest 1 0 0 0.078s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSparkIntegrationTest 1 0 0 0.382s 100%
org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalkerIntegrationTest 8 0 0 0.113s 100%
org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutorIntegrationTest 1 0 0 0.088s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceIntegrationTest 2 0 0 0.145s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSparkIntegrationTest 1 0 0 0.247s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsIntegrationTest 1 0 0 0.068s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSparkIntegrationTest 1 0 0 0.243s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest 1 0 0 0.022s 100%
org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalkerIntegrationTest 1 0 0 0.079s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerIntegrationTest 1 0 0 0.070s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSparkIntegrationTest 1 0 0 0.225s 100%
org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsIntegrationTest 18 0 0 1.287s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotateSegmentsIntegrationTest 6 0 0 13.493s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest 58 0 0 1m44.09s 100%
org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibilityIntegrationTest 16 0 0 0.943s 100%
org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest 23 0 0 2.020s 100%
org.broadinstitute.hellbender.tools.spark.ApplyBQSRSparkIntegrationTest 9 0 0 4.973s 100%
org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest 11 0 0 54.773s 100%
org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndexIntegrationTest 10 0 0 0.748s 100%
org.broadinstitute.hellbender.tools.spark.PileupSparkIntegrationTest 10 0 0 8.026s 100%
org.broadinstitute.hellbender.tools.spark.RevertSamSparkIntegrationTest 27 0 0 9.703s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaAndMarkDuplicatesPipelineSparkIntegrationTest 1 0 0 1.576s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkIntegrationTest 2 0 0 0.904s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmersSparkIntegrationTest 12 0 0 0.899s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomyIntegrationTest 5 0 0 0.363s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSparkIntegrationTest 1 0 0 1.426s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSparkIntegrationTest 6 0 0 9.008s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest 2 0 0 3.413s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreIntegrationTest 4 0 0 4.692s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest 3 0 0 5.328s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSparkIntegrationTest 7 0 0 1.485s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest 19 0 0 3.486s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSparkIntegrationTest 16 0 0 5.184s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSparkIntegrationTest 4 0 0 0.720s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest 152 0 0 59.468s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest 123 34 0 30.811s 72%
org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSparkIntegrationTest 13 0 0 2.811s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSparkIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSparkIntegrationTest 6 0 0 0.961s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest 8 0 0 1.021s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSparkIntegrationTest 6 0 0 1.058s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSparkIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.CpxVariantReInterpreterSparkIntegrationTest 2 0 0 8.321s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest 2 0 0 1.708s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest 2 0 0 0.866s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.FindBreakpointEvidenceSparkIntegrationTest 2 0 0 7.351s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.StructuralVariationDiscoveryPipelineSparkIntegrationTest 2 0 0 13.177s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest 2 0 0 5.344s 100%
org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest 6 0 0 3.378s 100%
org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidenceIntegrationTest 2 0 0 0.149s 100%
org.broadinstitute.hellbender.tools.sv.PrintReadCountsIntegrationTest 3 0 0 0.218s 100%
org.broadinstitute.hellbender.tools.sv.PrintSVEvidenceIntegrationTest 16 0 0 0.646s 100%
org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAFIntegrationTest 4 0 0 0.267s 100%
org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest 6 0 0 0.626s 100%
org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest 29 0 0 10.966s 100%
org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsIntegrationTest 98 0 0 49.985s 100%
org.broadinstitute.hellbender.tools.walkers.GnarlyGenotyperIntegrationTest 16 0 0 9.713s 100%
org.broadinstitute.hellbender.tools.walkers.MethylationTypeCallerIntegrationTest 1 0 0 0.111s 100%
org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest 4 0 0 1.681s 100%
org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScoresIntegrationTest 3 0 0 0.342s 100%
org.broadinstitute.hellbender.tools.walkers.SplitIntervalsIntegrationTest 9 0 0 1.620s 100%
org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicatesIntegrationTest 2 0 0 0.132s 100%
org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest 37 0 0 2.785s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.DirichletAlleleDepthAndFractionIntegrationTest 26 0 0 14.097s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorIntegrationTest 8 0 0 4.351s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariatesIntegrationTest 4 0 0 0.913s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSRIntegrationTest 24 0 0 11.839s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest 21 0 0 43.926s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest 1 0 0 44.955s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReportsIntegrationTest 2 0 0 16.727s 100%
org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSetIntegrationTest 2 0 0 0.822s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContaminationIntegrationTest 11 0 0 7.882s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummariesIntegrationTest 2 0 0 2.059s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummariesIntegrationTest 2 0 0 1.081s 100%
org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBedIntegrationTest 9 0 0 0.752s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.CallableLociIntegrationTest 1 0 0 15.740s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageIntegrationTest 7 0 0 24.639s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest 3 0 0 0.045s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest 17 0 0 1.314s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMakerIntegrationTest 6 0 0 0.469s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFastaIntegrationTest 2 0 0 0.219s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest 3 0 0 1.472s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperIntegrationTest 7 0 0 54.379s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypesIntegrationTest 3 0 0 1.793s 100%
org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltrationIntegrationTest 30 0 0 2.263s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQualityIntegrationTest 4 0 0 0.155s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilderIntegrationTest 3 0 0 9.215s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorerIntegrationTest 7 0 0 1.238s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentIntegrationTest 2 0 0 2.154s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHaplotypeIntegrationTest 1 0 0 0.024s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactDataIntegrationTest 1 0 0 5.700s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStatsIntegrationTest 1 0 0 0.069s 100%
org.broadinstitute.hellbender.tools.walkers.qc.CheckPileupIntegrationTest 2 0 0 0.177s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PileupIntegrationTest 5 0 0 0.357s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEMIntegrationTest 1 0 0 0.122s 100%
org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTagsIntegrationTest 5 0 0 0.448s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsIntegrationTest 3 0 0 0.664s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelIntegrationTest 4 0 0 37.921s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifactsIntegrationTest 1 0 0 2.354s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounterIntegrationTest 12 0 0 5.264s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluationIntegrationTest 11 0 0 11.322s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReadsIntegrationTest 9 0 0 15.394s 100%
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidenceIntegrationTest 4 0 0 6.134s 100%
org.broadinstitute.hellbender.tools.walkers.sv.GroupedSVClusterIntegrationTest 1 0 0 1.115s 100%
org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentationIntegrationTest 3 0 0 0.747s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest 6 0 0 2.133s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVClusterIntegrationTest 10 0 0 8.912s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVConcordanceIntegrationTest 9 0 0 16.297s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVStratifyIntegrationTest 5 0 0 0.695s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepthIntegrationTest 1 0 0 0.143s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFractionIntegrationTest 1 0 0 0.101s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractionsIntegrationTest 1 0 0 0.165s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceIntegrationTest 6 0 0 0.562s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositivesIntegrationTest 2 0 0 0.268s 100%
org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordanceIntegrationTest 2 0 0 0.181s 100%
org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3IntegrationTest 1 0 0 0.113s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordanceIntegrationTest 16 0 0 1.414s 100%
org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndelsIntegrationTest 1 0 0 0.075s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest 2 0 0 0.812s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest 45 0 0 16.650s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerIntegrationTest 2 0 0 0.960s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriorsIntegrationTest 14 0 0 1.968s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest 9 0 0 0.740s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest 32 0 0 12.481s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest 88 0 0 6.520s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionaryIntegrationTest 14 0 0 0.972s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest 17 0 0 3.308s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTableIntegrationTest 21 0 0 1.614s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSRIntegrationTest 7 0 0 3.102s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranchesIntegrationTest 4 0 0 0.303s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorIntegrationTest 16 0 0 35.449s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest 5 0 0 0.850s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotationsIntegrationTest 2 0 0 0.169s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest 2 0 0 0.095s 100%
org.broadinstitute.hellbender.utils.config.ConfigIntegrationTest 2 0 0 0.165s 100%
org.broadinstitute.hellbender.utils.config.ConfigPrintReadsIntegrationTest 1 0 0 0.282s 100%
org.broadinstitute.hellbender.utils.help.DocumentationGenerationIntegrationTest 1 0 0 5.364s 100%
org.broadinstitute.hellbender.utils.help.TabCompletionIntegrationTest 1 0 0 6.373s 100%
org.broadinstitute.hellbender.utils.help.WDLGenerationIntegrationTest 2 0 0 4.135s 100%
org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest 1 0 0 0.153s 100%
org.broadinstitute.hellbender.utils.read.FlowBasedReadIntegrationTest 1 0 0 0.068s 100%