Test Summary

2073

tests
2

failures
8

ignored
25m12.86s

duration
99%

successful

Ignored tests

Packages

Package Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender 11 2 0 2.299s 81%
org.broadinstitute.hellbender.cmdline 7 0 0 0.409s 100%
org.broadinstitute.hellbender.engine 114 0 0 1m27.73s 100%
org.broadinstitute.hellbender.engine.filters.flow 2 0 0 0.408s 100%
org.broadinstitute.hellbender.engine.spark 1 0 0 0.095s 100%
org.broadinstitute.hellbender.tools 275 0 0 2m56.86s 100%
org.broadinstitute.hellbender.tools.copynumber 184 0 0 1m8.14s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting 20 0 0 1.643s 100%
org.broadinstitute.hellbender.tools.copynumber.utils 23 0 0 2.096s 100%
org.broadinstitute.hellbender.tools.dragstr 15 0 0 3m35.47s 100%
org.broadinstitute.hellbender.tools.examples 30 0 0 7.364s 100%
org.broadinstitute.hellbender.tools.funcotator 82 0 0 1m58.10s 100%
org.broadinstitute.hellbender.tools.reference 39 0 0 4.063s 100%
org.broadinstitute.hellbender.tools.spark 67 0 2 1m34.78s 100%
org.broadinstitute.hellbender.tools.spark.bwa 3 0 0 2.521s 100%
org.broadinstitute.hellbender.tools.spark.pathseq 30 0 0 20.266s 100%
org.broadinstitute.hellbender.tools.spark.pipelines 279 0 1 1m38.52s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics 22 0 0 3.327s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration 12 0 4 14.198s 100%
org.broadinstitute.hellbender.tools.spark.validation 6 0 0 3.392s 100%
org.broadinstitute.hellbender.tools.sv 25 0 0 1.712s 100%
org.broadinstitute.hellbender.tools.validation 6 0 0 0.682s 100%
org.broadinstitute.hellbender.tools.walkers 199 0 0 1m19.82s 100%
org.broadinstitute.hellbender.tools.walkers.annotator 34 0 0 17.845s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr 52 0 0 2m31.79s 100%
org.broadinstitute.hellbender.tools.walkers.consensus 2 0 0 0.872s 100%
org.broadinstitute.hellbender.tools.walkers.contamination 15 0 0 11.501s 100%
org.broadinstitute.hellbender.tools.walkers.conversion 9 0 0 0.926s 100%
org.broadinstitute.hellbender.tools.walkers.coverage 8 0 0 38.703s 100%
org.broadinstitute.hellbender.tools.walkers.fasta 28 0 0 2.482s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping 13 0 0 59.123s 100%
org.broadinstitute.hellbender.tools.walkers.filters 30 0 0 2.819s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth 14 0 0 11.196s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller 3 0 0 2.135s 100%
org.broadinstitute.hellbender.tools.walkers.mutect 2 0 0 5.841s 100%
org.broadinstitute.hellbender.tools.walkers.qc 13 0 0 1.324s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation 7 0 0 38.349s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter 1 0 0 2.231s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq 32 0 0 34.807s 100%
org.broadinstitute.hellbender.tools.walkers.sv 38 0 0 36.036s 100%
org.broadinstitute.hellbender.tools.walkers.validation 31 0 0 3.316s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup 2 0 0 1.044s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval 45 0 0 17.037s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling 2 0 0 0.926s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils 195 0 0 30.831s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr 27 0 0 36.249s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable 9 0 0 0.939s 100%
org.broadinstitute.hellbender.utils.config 3 0 0 0.573s 100%
org.broadinstitute.hellbender.utils.help 4 0 0 0s 100%
org.broadinstitute.hellbender.utils.python 1 0 1 0s -
org.broadinstitute.hellbender.utils.read 1 0 0 0.080s 100%

Classes

Class Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender.BwaMemIntegrationTest 2 2 0 0.001s 0%
org.broadinstitute.hellbender.IntelInflaterDeflaterIntegrationTest 6 0 0 1.949s 100%
org.broadinstitute.hellbender.PrintFileDiagnosticsIntegrationTest 3 0 0 0.349s 100%
org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidatorIntegrationTest 2 0 0 0.180s 100%
org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest 3 0 0 0.033s 100%
org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutorIntegrationTest 2 0 0 0.196s 100%
org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest 45 0 0 1m15.72s 100%
org.broadinstitute.hellbender.engine.FeatureSupportIntegrationTest 6 0 0 0.572s 100%
org.broadinstitute.hellbender.engine.GatkToolIntegrationTest 22 0 0 2.054s 100%
org.broadinstitute.hellbender.engine.GenomicsDBIntegrationTest 7 0 0 2.079s 100%
org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest 15 0 0 0.333s 100%
org.broadinstitute.hellbender.engine.PartialReadWalkerIntegrationTest 2 0 0 0.087s 100%
org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest 1 0 0 2.998s 100%
org.broadinstitute.hellbender.engine.ReadWalkerIntegrationTest 2 0 0 0.168s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationSparkIntegrationTest 3 0 0 2.929s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationWalkerIntegrationTest 3 0 0 0.313s 100%
org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest 7 0 0 0.367s 100%
org.broadinstitute.hellbender.engine.WalkerOutputIntegrationTest 1 0 0 0.111s 100%
org.broadinstitute.hellbender.engine.filters.flow.WellFormedFlowBasedReadFilterIntegrationTest 2 0 0 0.408s 100%
org.broadinstitute.hellbender.engine.spark.GATKSparkToolIntegrationTest 1 0 0 0.095s 100%
org.broadinstitute.hellbender.tools.AddOriginalAlignmentTagsIntegrationTest 2 0 0 0.283s 100%
org.broadinstitute.hellbender.tools.BwaMemIndexImageCreatorIntegrationTest 1 0 0 2m3.45s 100%
org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotationsIntegrationTest 2 0 0 0.196s 100%
org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest 17 0 0 2.008s 100%
org.broadinstitute.hellbender.tools.CompareIntervalListsIntegrationTest 10 0 0 0.788s 100%
org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBamIntegrationTest 1 0 0 0.078s 100%
org.broadinstitute.hellbender.tools.CountBasesIntegrationTest 6 0 0 0.556s 100%
org.broadinstitute.hellbender.tools.CountReadsIntegrationTest 38 0 0 3.470s 100%
org.broadinstitute.hellbender.tools.CountVariantsIntegrationTest 10 0 0 7.608s 100%
org.broadinstitute.hellbender.tools.DumpTabixIndexIntegrationTest 1 0 0 0.108s 100%
org.broadinstitute.hellbender.tools.FlagStatIntegrationTest 6 0 0 0.468s 100%
org.broadinstitute.hellbender.tools.GatherVcfsCloudIntegrationTest 12 0 0 1.455s 100%
org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest 3 0 0 0.359s 100%
org.broadinstitute.hellbender.tools.HtsgetReaderIntegrationTest 3 0 0 16.544s 100%
org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest 25 0 0 2.176s 100%
org.broadinstitute.hellbender.tools.LeftAlignIndelsIntegrationTest 1 0 0 0.199s 100%
org.broadinstitute.hellbender.tools.PrintBGZFBlockInformationIntegrationTest 8 0 0 0.671s 100%
org.broadinstitute.hellbender.tools.PrintReadsHeaderIntegrationTest 1 0 0 0.091s 100%
org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest 91 0 0 11.314s 100%
org.broadinstitute.hellbender.tools.SplitCRAMIntegrationTest 2 0 0 0.092s 100%
org.broadinstitute.hellbender.tools.SplitReadsIntegrationTest 35 0 0 4.946s 100%
org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervalsIntegrationTest 9 0 0 1.049s 100%
org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegmentsIntegrationTest 1 0 0 0.091s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsIntegrationTest 4 0 0 0.457s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest 4 0 0 2.459s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectReadCountsIntegrationTest 6 0 0 0.716s 100%
org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormalsIntegrationTest 36 0 0 10.788s 100%
org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest 48 0 0 3.782s 100%
org.broadinstitute.hellbender.tools.copynumber.FilterIntervalsIntegrationTest 30 0 0 2.781s 100%
org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCallerIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.tools.copynumber.ModelSegmentsIntegrationTest 33 0 0 44.558s 100%
org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervalsIntegrationTest 12 0 0 1.456s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatiosIntegrationTest 7 0 0 0.597s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegmentsIntegrationTest 13 0 0 1.046s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpointsIntegrationTest 15 0 0 1.390s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotationIntegrationTest 1 0 0 0.089s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsIntegrationTest 2 0 0 0.169s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEventsIntegrationTest 5 0 0 0.448s 100%
org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModelIntegrationTest 12 0 0 2m30.74s 100%
org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFileIntegrationTest 3 0 0 1m4.73s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerIntegrationTest 1 0 0 0.938s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest 2 0 0 2.808s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectMultiMetricsIntegrationTest 2 0 0 0.656s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectSingleMetricsIntegrationTest 1 0 0 0.218s 100%
org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalkerIntegrationTest 2 0 0 0.179s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerIntegrationTest 1 0 0 0.100s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSparkIntegrationTest 1 0 0 0.397s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerIntegrationTest 1 0 0 0.097s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSparkIntegrationTest 1 0 0 0.393s 100%
org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalkerIntegrationTest 8 0 0 0.204s 100%
org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutorIntegrationTest 1 0 0 0.110s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceIntegrationTest 2 0 0 0.188s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSparkIntegrationTest 1 0 0 0.253s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsIntegrationTest 1 0 0 0.088s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSparkIntegrationTest 1 0 0 0.272s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest 1 0 0 0.030s 100%
org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalkerIntegrationTest 1 0 0 0.110s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerIntegrationTest 1 0 0 0.089s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSparkIntegrationTest 1 0 0 0.234s 100%
org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsIntegrationTest 18 0 0 1.709s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotateSegmentsIntegrationTest 6 0 0 14.299s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest 58 0 0 1m42.09s 100%
org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibilityIntegrationTest 16 0 0 1.369s 100%
org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest 23 0 0 2.694s 100%
org.broadinstitute.hellbender.tools.spark.ApplyBQSRSparkIntegrationTest 9 0 0 5.757s 100%
org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest 11 0 0 1m15.05s 100%
org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndexIntegrationTest 10 0 0 0.816s 100%
org.broadinstitute.hellbender.tools.spark.PileupSparkIntegrationTest 10 0 2 3.873s 100%
org.broadinstitute.hellbender.tools.spark.RevertSamSparkIntegrationTest 27 0 0 9.289s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaAndMarkDuplicatesPipelineSparkIntegrationTest 1 0 0 1.560s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkIntegrationTest 2 0 0 0.961s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmersSparkIntegrationTest 12 0 0 1.079s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomyIntegrationTest 5 0 0 0.412s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSparkIntegrationTest 1 0 0 1.293s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSparkIntegrationTest 6 0 0 9.081s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest 2 0 0 3.513s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreIntegrationTest 4 0 0 4.888s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest 3 0 0 5.447s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSparkIntegrationTest 7 0 0 1.493s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest 19 0 0 3.820s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSparkIntegrationTest 16 0 0 5.402s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSparkIntegrationTest 4 0 0 0.794s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest 152 0 0 58.715s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest 65 0 1 20.020s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSparkIntegrationTest 13 0 0 2.829s 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 1.044s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest 8 0 0 1.144s 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 0 1 1.284s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest 2 0 1 0.370s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest 2 0 0 0.847s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.FindBreakpointEvidenceSparkIntegrationTest 2 0 1 2.581s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.StructuralVariationDiscoveryPipelineSparkIntegrationTest 2 0 1 3.051s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest 2 0 0 6.065s 100%
org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest 6 0 0 3.392s 100%
org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidenceIntegrationTest 2 0 0 0.191s 100%
org.broadinstitute.hellbender.tools.sv.PrintReadCountsIntegrationTest 3 0 0 0.288s 100%
org.broadinstitute.hellbender.tools.sv.PrintSVEvidenceIntegrationTest 16 0 0 0.864s 100%
org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAFIntegrationTest 4 0 0 0.369s 100%
org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest 6 0 0 0.682s 100%
org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest 29 0 0 10.134s 100%
org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsIntegrationTest 98 0 0 50.675s 100%
org.broadinstitute.hellbender.tools.walkers.GnarlyGenotyperIntegrationTest 16 0 0 11.143s 100%
org.broadinstitute.hellbender.tools.walkers.MethylationTypeCallerIntegrationTest 1 0 0 0.118s 100%
org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest 4 0 0 1.920s 100%
org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScoresIntegrationTest 3 0 0 0.396s 100%
org.broadinstitute.hellbender.tools.walkers.SplitIntervalsIntegrationTest 9 0 0 1.574s 100%
org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicatesIntegrationTest 2 0 0 0.174s 100%
org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest 37 0 0 3.681s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.DirichletAlleleDepthAndFractionIntegrationTest 26 0 0 13.336s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorIntegrationTest 8 0 0 4.509s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariatesIntegrationTest 4 0 0 0.906s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSRIntegrationTest 24 0 0 10.904s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest 21 0 0 1m1.66s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest 1 0 0 55.316s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReportsIntegrationTest 2 0 0 22.998s 100%
org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSetIntegrationTest 2 0 0 0.872s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContaminationIntegrationTest 11 0 0 7.993s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummariesIntegrationTest 2 0 0 2.429s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummariesIntegrationTest 2 0 0 1.079s 100%
org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBedIntegrationTest 9 0 0 0.926s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.CallableLociIntegrationTest 1 0 0 15.018s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageIntegrationTest 7 0 0 23.685s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest 3 0 0 0.079s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest 17 0 0 1.584s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMakerIntegrationTest 6 0 0 0.562s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFastaIntegrationTest 2 0 0 0.257s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest 3 0 0 1.671s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperIntegrationTest 7 0 0 55.678s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypesIntegrationTest 3 0 0 1.774s 100%
org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltrationIntegrationTest 30 0 0 2.819s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQualityIntegrationTest 4 0 0 0.227s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilderIntegrationTest 3 0 0 9.685s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorerIntegrationTest 7 0 0 1.284s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentIntegrationTest 2 0 0 2.110s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHaplotypeIntegrationTest 1 0 0 0.025s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactDataIntegrationTest 1 0 0 5.768s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStatsIntegrationTest 1 0 0 0.073s 100%
org.broadinstitute.hellbender.tools.walkers.qc.CheckPileupIntegrationTest 2 0 0 0.221s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PileupIntegrationTest 5 0 0 0.439s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEMIntegrationTest 1 0 0 0.137s 100%
org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTagsIntegrationTest 5 0 0 0.527s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsIntegrationTest 3 0 0 0.747s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelIntegrationTest 4 0 0 37.602s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifactsIntegrationTest 1 0 0 2.231s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounterIntegrationTest 12 0 0 5.254s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluationIntegrationTest 11 0 0 14.420s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReadsIntegrationTest 9 0 0 15.133s 100%
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidenceIntegrationTest 4 0 0 6.118s 100%
org.broadinstitute.hellbender.tools.walkers.sv.GroupedSVClusterIntegrationTest 1 0 0 1.087s 100%
org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentationIntegrationTest 3 0 0 0.788s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest 6 0 0 2.257s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVClusterIntegrationTest 10 0 0 8.905s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVConcordanceIntegrationTest 9 0 0 16.015s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVStratifyIntegrationTest 5 0 0 0.866s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepthIntegrationTest 1 0 0 0.127s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFractionIntegrationTest 1 0 0 0.090s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractionsIntegrationTest 1 0 0 0.101s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceIntegrationTest 6 0 0 0.661s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositivesIntegrationTest 2 0 0 0.313s 100%
org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordanceIntegrationTest 2 0 0 0.225s 100%
org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3IntegrationTest 1 0 0 0.121s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordanceIntegrationTest 16 0 0 1.586s 100%
org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndelsIntegrationTest 1 0 0 0.092s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest 2 0 0 1.044s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest 45 0 0 17.037s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerIntegrationTest 2 0 0 0.926s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriorsIntegrationTest 14 0 0 2.398s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest 9 0 0 0.917s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest 32 0 0 12.554s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest 88 0 0 8.130s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionaryIntegrationTest 14 0 0 1.215s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest 17 0 0 3.615s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTableIntegrationTest 21 0 0 2.002s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSRIntegrationTest 7 0 0 2.880s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranchesIntegrationTest 4 0 0 0.331s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorIntegrationTest 16 0 0 33.038s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest 5 0 0 0.722s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotationsIntegrationTest 2 0 0 0.136s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest 2 0 0 0.081s 100%
org.broadinstitute.hellbender.utils.config.ConfigIntegrationTest 2 0 0 0.186s 100%
org.broadinstitute.hellbender.utils.config.ConfigPrintReadsIntegrationTest 1 0 0 0.387s 100%
org.broadinstitute.hellbender.utils.help.DocumentationGenerationIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.utils.help.TabCompletionIntegrationTest 1 0 0 0s 100%
org.broadinstitute.hellbender.utils.help.WDLGenerationIntegrationTest 2 0 0 0s 100%
org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest 1 0 1 0s -
org.broadinstitute.hellbender.utils.read.FlowBasedReadIntegrationTest 1 0 0 0.080s 100%