Test Summary

2071

tests
7

failures
0

ignored
23m17.81s

duration
99%

successful

Failed tests

Packages

Package Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender 11 0 0 2.076s 100%
org.broadinstitute.hellbender.cmdline 7 0 0 0.328s 100%
org.broadinstitute.hellbender.engine 114 0 0 1m29.60s 100%
org.broadinstitute.hellbender.engine.filters.flow 2 0 0 0.411s 100%
org.broadinstitute.hellbender.engine.spark 1 0 0 0.087s 100%
org.broadinstitute.hellbender.tools 275 0 0 2m43.11s 100%
org.broadinstitute.hellbender.tools.copynumber 184 0 0 1m3.56s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting 20 0 0 1.240s 100%
org.broadinstitute.hellbender.tools.copynumber.utils 23 0 0 1.463s 100%
org.broadinstitute.hellbender.tools.dragstr 15 0 0 3m3.25s 100%
org.broadinstitute.hellbender.tools.examples 30 0 0 7.056s 100%
org.broadinstitute.hellbender.tools.funcotator 82 0 0 1m52.41s 100%
org.broadinstitute.hellbender.tools.reference 39 0 0 2.986s 100%
org.broadinstitute.hellbender.tools.spark 67 2 0 1m15.47s 97%
org.broadinstitute.hellbender.tools.spark.bwa 3 0 0 2.694s 100%
org.broadinstitute.hellbender.tools.spark.pathseq 30 0 0 20.416s 100%
org.broadinstitute.hellbender.tools.spark.pipelines 279 1 0 1m45.26s 99%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics 22 0 0 3.182s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration 12 4 0 16.327s 66%
org.broadinstitute.hellbender.tools.spark.validation 6 0 0 3.556s 100%
org.broadinstitute.hellbender.tools.sv 25 0 0 1.246s 100%
org.broadinstitute.hellbender.tools.validation 6 0 0 0.652s 100%
org.broadinstitute.hellbender.tools.walkers 199 0 0 1m15.57s 100%
org.broadinstitute.hellbender.tools.walkers.annotator 34 0 0 16.129s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr 52 0 0 1m54.14s 100%
org.broadinstitute.hellbender.tools.walkers.consensus 2 0 0 0.766s 100%
org.broadinstitute.hellbender.tools.walkers.contamination 15 0 0 10.592s 100%
org.broadinstitute.hellbender.tools.walkers.conversion 9 0 0 0.730s 100%
org.broadinstitute.hellbender.tools.walkers.coverage 8 0 0 38.871s 100%
org.broadinstitute.hellbender.tools.walkers.fasta 28 0 0 1.913s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping 13 0 0 57.672s 100%
org.broadinstitute.hellbender.tools.walkers.filters 30 0 0 2.093s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth 14 0 0 10.578s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller 3 0 0 2.130s 100%
org.broadinstitute.hellbender.tools.walkers.mutect 2 0 0 5.670s 100%
org.broadinstitute.hellbender.tools.walkers.qc 13 0 0 0.968s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation 7 0 0 38.567s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter 1 0 0 2.252s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq 32 0 0 34.540s 100%
org.broadinstitute.hellbender.tools.walkers.sv 36 0 0 28.557s 100%
org.broadinstitute.hellbender.tools.walkers.validation 31 0 0 2.865s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup 2 0 0 0.887s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval 45 0 0 16.771s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling 2 0 0 0.833s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils 195 0 0 26.137s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr 27 0 0 36.440s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable 9 0 0 0.928s 100%
org.broadinstitute.hellbender.utils.config 3 0 0 0.460s 100%
org.broadinstitute.hellbender.utils.help 4 0 0 14.055s 100%
org.broadinstitute.hellbender.utils.python 1 0 0 0.237s 100%
org.broadinstitute.hellbender.utils.read 1 0 0 0.070s 100%

Classes

Class Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender.BwaMemIntegrationTest 2 0 0 0.226s 100%
org.broadinstitute.hellbender.IntelInflaterDeflaterIntegrationTest 6 0 0 1.564s 100%
org.broadinstitute.hellbender.PrintFileDiagnosticsIntegrationTest 3 0 0 0.286s 100%
org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidatorIntegrationTest 2 0 0 0.136s 100%
org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest 3 0 0 0.036s 100%
org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutorIntegrationTest 2 0 0 0.156s 100%
org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest 45 0 0 1m18.62s 100%
org.broadinstitute.hellbender.engine.FeatureSupportIntegrationTest 6 0 0 0.445s 100%
org.broadinstitute.hellbender.engine.GatkToolIntegrationTest 22 0 0 1.543s 100%
org.broadinstitute.hellbender.engine.GenomicsDBIntegrationTest 7 0 0 1.507s 100%
org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest 15 0 0 0.158s 100%
org.broadinstitute.hellbender.engine.PartialReadWalkerIntegrationTest 2 0 0 0.073s 100%
org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest 1 0 0 3.119s 100%
org.broadinstitute.hellbender.engine.ReadWalkerIntegrationTest 2 0 0 0.132s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationSparkIntegrationTest 3 0 0 3.330s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationWalkerIntegrationTest 3 0 0 0.242s 100%
org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest 7 0 0 0.302s 100%
org.broadinstitute.hellbender.engine.WalkerOutputIntegrationTest 1 0 0 0.129s 100%
org.broadinstitute.hellbender.engine.filters.flow.WellFormedFlowBasedReadFilterIntegrationTest 2 0 0 0.411s 100%
org.broadinstitute.hellbender.engine.spark.GATKSparkToolIntegrationTest 1 0 0 0.087s 100%
org.broadinstitute.hellbender.tools.AddOriginalAlignmentTagsIntegrationTest 2 0 0 0.196s 100%
org.broadinstitute.hellbender.tools.BwaMemIndexImageCreatorIntegrationTest 1 0 0 2m7.59s 100%
org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotationsIntegrationTest 2 0 0 0.175s 100%
org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest 17 0 0 1.390s 100%
org.broadinstitute.hellbender.tools.CompareIntervalListsIntegrationTest 10 0 0 0.639s 100%
org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBamIntegrationTest 1 0 0 0.057s 100%
org.broadinstitute.hellbender.tools.CountBasesIntegrationTest 6 0 0 0.360s 100%
org.broadinstitute.hellbender.tools.CountReadsIntegrationTest 38 0 0 2.334s 100%
org.broadinstitute.hellbender.tools.CountVariantsIntegrationTest 10 0 0 7.051s 100%
org.broadinstitute.hellbender.tools.DumpTabixIndexIntegrationTest 1 0 0 0.074s 100%
org.broadinstitute.hellbender.tools.FlagStatIntegrationTest 6 0 0 0.268s 100%
org.broadinstitute.hellbender.tools.GatherVcfsCloudIntegrationTest 12 0 0 0.976s 100%
org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest 3 0 0 0.216s 100%
org.broadinstitute.hellbender.tools.HtsgetReaderIntegrationTest 3 0 0 5.953s 100%
org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest 25 0 0 1.880s 100%
org.broadinstitute.hellbender.tools.LeftAlignIndelsIntegrationTest 1 0 0 0.173s 100%
org.broadinstitute.hellbender.tools.PrintBGZFBlockInformationIntegrationTest 8 0 0 0.498s 100%
org.broadinstitute.hellbender.tools.PrintReadsHeaderIntegrationTest 1 0 0 0.063s 100%
org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest 91 0 0 9.234s 100%
org.broadinstitute.hellbender.tools.SplitCRAMIntegrationTest 2 0 0 0.067s 100%
org.broadinstitute.hellbender.tools.SplitReadsIntegrationTest 35 0 0 3.918s 100%
org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervalsIntegrationTest 9 0 0 0.740s 100%
org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegmentsIntegrationTest 1 0 0 0.082s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsIntegrationTest 4 0 0 0.327s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest 4 0 0 2.593s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectReadCountsIntegrationTest 6 0 0 0.467s 100%
org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormalsIntegrationTest 36 0 0 10.304s 100%
org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest 48 0 0 2.966s 100%
org.broadinstitute.hellbender.tools.copynumber.FilterIntervalsIntegrationTest 30 0 0 2.067s 100%
org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCallerIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.copynumber.ModelSegmentsIntegrationTest 33 0 0 42.914s 100%
org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervalsIntegrationTest 12 0 0 1.096s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatiosIntegrationTest 7 0 0 0.450s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegmentsIntegrationTest 13 0 0 0.790s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpointsIntegrationTest 15 0 0 0.977s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotationIntegrationTest 1 0 0 0.062s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsIntegrationTest 2 0 0 0.117s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEventsIntegrationTest 5 0 0 0.307s 100%
org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModelIntegrationTest 12 0 0 1m56.57s 100%
org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFileIntegrationTest 3 0 0 1m6.68s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerIntegrationTest 1 0 0 1.011s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest 2 0 0 2.795s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectMultiMetricsIntegrationTest 2 0 0 0.627s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectSingleMetricsIntegrationTest 1 0 0 0.204s 100%
org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalkerIntegrationTest 2 0 0 0.137s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerIntegrationTest 1 0 0 0.074s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSparkIntegrationTest 1 0 0 0.419s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSparkIntegrationTest 1 0 0 0.419s 100%
org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalkerIntegrationTest 8 0 0 0.122s 100%
org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutorIntegrationTest 1 0 0 0.088s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceIntegrationTest 2 0 0 0.123s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSparkIntegrationTest 1 0 0 0.240s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsIntegrationTest 1 0 0 0.065s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSparkIntegrationTest 1 0 0 0.248s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest 1 0 0 0.019s 100%
org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalkerIntegrationTest 1 0 0 0.083s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerIntegrationTest 1 0 0 0.068s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSparkIntegrationTest 1 0 0 0.243s 100%
org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsIntegrationTest 18 0 0 1.214s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotateSegmentsIntegrationTest 6 0 0 14.073s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest 58 0 0 1m37.13s 100%
org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibilityIntegrationTest 16 0 0 0.960s 100%
org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest 23 0 0 2.026s 100%
org.broadinstitute.hellbender.tools.spark.ApplyBQSRSparkIntegrationTest 9 0 0 5.273s 100%
org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest 11 0 0 54.409s 100%
org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndexIntegrationTest 10 0 0 0.611s 100%
org.broadinstitute.hellbender.tools.spark.PileupSparkIntegrationTest 10 2 0 4.895s 80%
org.broadinstitute.hellbender.tools.spark.RevertSamSparkIntegrationTest 27 0 0 10.286s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaAndMarkDuplicatesPipelineSparkIntegrationTest 1 0 0 1.648s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkIntegrationTest 2 0 0 1.046s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmersSparkIntegrationTest 12 0 0 0.863s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomyIntegrationTest 5 0 0 0.344s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSparkIntegrationTest 1 0 0 1.422s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSparkIntegrationTest 6 0 0 9.207s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest 2 0 0 3.476s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreIntegrationTest 4 0 0 5.104s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest 3 0 0 5.664s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSparkIntegrationTest 7 0 0 1.633s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest 19 0 0 3.824s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSparkIntegrationTest 16 0 0 5.211s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSparkIntegrationTest 4 0 0 0.749s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest 152 0 0 1m3.03s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest 65 1 0 22.234s 98%
org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSparkIntegrationTest 13 0 0 2.919s 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 1.016s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest 8 0 0 1.027s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSparkIntegrationTest 6 0 0 1.139s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSparkIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.CpxVariantReInterpreterSparkIntegrationTest 2 1 0 1.707s 50%
org.broadinstitute.hellbender.tools.spark.sv.integration.DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest 2 1 0 0.697s 50%
org.broadinstitute.hellbender.tools.spark.sv.integration.ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest 2 0 0 0.867s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.FindBreakpointEvidenceSparkIntegrationTest 2 1 0 2.983s 50%
org.broadinstitute.hellbender.tools.spark.sv.integration.StructuralVariationDiscoveryPipelineSparkIntegrationTest 2 1 0 4.298s 50%
org.broadinstitute.hellbender.tools.spark.sv.integration.SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest 2 0 0 5.775s 100%
org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest 6 0 0 3.556s 100%
org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidenceIntegrationTest 2 0 0 0.199s 100%
org.broadinstitute.hellbender.tools.sv.PrintReadCountsIntegrationTest 3 0 0 0.204s 100%
org.broadinstitute.hellbender.tools.sv.PrintSVEvidenceIntegrationTest 16 0 0 0.595s 100%
org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAFIntegrationTest 4 0 0 0.248s 100%
org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest 6 0 0 0.652s 100%
org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest 29 0 0 10.498s 100%
org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsIntegrationTest 98 0 0 48.880s 100%
org.broadinstitute.hellbender.tools.walkers.GnarlyGenotyperIntegrationTest 16 0 0 9.824s 100%
org.broadinstitute.hellbender.tools.walkers.MethylationTypeCallerIntegrationTest 1 0 0 0.106s 100%
org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest 4 0 0 1.683s 100%
org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScoresIntegrationTest 3 0 0 0.355s 100%
org.broadinstitute.hellbender.tools.walkers.SplitIntervalsIntegrationTest 9 0 0 1.340s 100%
org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicatesIntegrationTest 2 0 0 0.129s 100%
org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest 37 0 0 2.757s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.DirichletAlleleDepthAndFractionIntegrationTest 26 0 0 12.444s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorIntegrationTest 8 0 0 3.685s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariatesIntegrationTest 4 0 0 0.936s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSRIntegrationTest 24 0 0 9.675s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest 21 0 0 43.210s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest 1 0 0 43.752s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReportsIntegrationTest 2 0 0 16.562s 100%
org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSetIntegrationTest 2 0 0 0.766s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContaminationIntegrationTest 11 0 0 7.554s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummariesIntegrationTest 2 0 0 1.952s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummariesIntegrationTest 2 0 0 1.086s 100%
org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBedIntegrationTest 9 0 0 0.730s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.CallableLociIntegrationTest 1 0 0 15.099s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageIntegrationTest 7 0 0 23.772s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest 3 0 0 0.046s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest 17 0 0 1.248s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMakerIntegrationTest 6 0 0 0.428s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFastaIntegrationTest 2 0 0 0.191s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest 3 0 0 1.569s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperIntegrationTest 7 0 0 54.371s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypesIntegrationTest 3 0 0 1.732s 100%
org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltrationIntegrationTest 30 0 0 2.093s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQualityIntegrationTest 4 0 0 0.206s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilderIntegrationTest 3 0 0 9.218s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorerIntegrationTest 7 0 0 1.154s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentIntegrationTest 2 0 0 2.105s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHaplotypeIntegrationTest 1 0 0 0.025s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactDataIntegrationTest 1 0 0 5.598s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStatsIntegrationTest 1 0 0 0.072s 100%
org.broadinstitute.hellbender.tools.walkers.qc.CheckPileupIntegrationTest 2 0 0 0.172s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PileupIntegrationTest 5 0 0 0.329s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEMIntegrationTest 1 0 0 0.114s 100%
org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTagsIntegrationTest 5 0 0 0.353s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsIntegrationTest 3 0 0 0.629s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelIntegrationTest 4 0 0 37.938s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifactsIntegrationTest 1 0 0 2.252s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounterIntegrationTest 12 0 0 5.149s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluationIntegrationTest 11 0 0 14.254s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReadsIntegrationTest 9 0 0 15.137s 100%
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidenceIntegrationTest 4 0 0 5.871s 100%
org.broadinstitute.hellbender.tools.walkers.sv.GroupedSVClusterIntegrationTest 1 0 0 0.987s 100%
org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentationIntegrationTest 3 0 0 0.766s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest 6 0 0 2.081s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVClusterIntegrationTest 10 0 0 9.213s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVConcordanceIntegrationTest 7 0 0 8.959s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVStratifyIntegrationTest 5 0 0 0.680s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepthIntegrationTest 1 0 0 0.105s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFractionIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractionsIntegrationTest 1 0 0 0.083s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceIntegrationTest 6 0 0 0.739s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositivesIntegrationTest 2 0 0 0.304s 100%
org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordanceIntegrationTest 2 0 0 0.194s 100%
org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3IntegrationTest 1 0 0 0.114s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordanceIntegrationTest 16 0 0 1.182s 100%
org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndelsIntegrationTest 1 0 0 0.073s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest 2 0 0 0.887s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest 45 0 0 16.771s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerIntegrationTest 2 0 0 0.833s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriorsIntegrationTest 14 0 0 1.884s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest 9 0 0 0.710s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest 32 0 0 11.782s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest 88 0 0 6.253s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionaryIntegrationTest 14 0 0 0.910s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest 17 0 0 3.075s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTableIntegrationTest 21 0 0 1.523s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSRIntegrationTest 7 0 0 2.784s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranchesIntegrationTest 4 0 0 0.274s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorIntegrationTest 16 0 0 33.382s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest 5 0 0 0.755s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotationsIntegrationTest 2 0 0 0.107s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest 2 0 0 0.066s 100%
org.broadinstitute.hellbender.utils.config.ConfigIntegrationTest 2 0 0 0.139s 100%
org.broadinstitute.hellbender.utils.config.ConfigPrintReadsIntegrationTest 1 0 0 0.321s 100%
org.broadinstitute.hellbender.utils.help.DocumentationGenerationIntegrationTest 1 0 0 5.249s 100%
org.broadinstitute.hellbender.utils.help.TabCompletionIntegrationTest 1 0 0 5.095s 100%
org.broadinstitute.hellbender.utils.help.WDLGenerationIntegrationTest 2 0 0 3.711s 100%
org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest 1 0 0 0.237s 100%
org.broadinstitute.hellbender.utils.read.FlowBasedReadIntegrationTest 1 0 0 0.070s 100%