Test Summary

2210

tests
1

failures
26

ignored
25m12.50s

duration
99%

successful

Ignored tests

Packages

Package Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender 11 0 0 2.526s 100%
org.broadinstitute.hellbender.cmdline 7 0 0 0.380s 100%
org.broadinstitute.hellbender.engine 116 0 1 1m27.94s 100%
org.broadinstitute.hellbender.engine.filters.flow 2 0 0 0.413s 100%
org.broadinstitute.hellbender.engine.spark 1 0 0 0.106s 100%
org.broadinstitute.hellbender.tools 364 0 0 2m51.69s 100%
org.broadinstitute.hellbender.tools.copynumber 187 0 0 1m8.97s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting 22 0 0 1.847s 100%
org.broadinstitute.hellbender.tools.copynumber.utils 23 0 0 2.136s 100%
org.broadinstitute.hellbender.tools.dragstr 15 0 0 3m33.86s 100%
org.broadinstitute.hellbender.tools.examples 32 0 0 8.051s 100%
org.broadinstitute.hellbender.tools.funcotator 82 0 0 1m54.10s 100%
org.broadinstitute.hellbender.tools.reference 39 0 0 4.407s 100%
org.broadinstitute.hellbender.tools.spark 67 0 2 1m33.37s 100%
org.broadinstitute.hellbender.tools.spark.bwa 3 0 0 2.617s 100%
org.broadinstitute.hellbender.tools.spark.pathseq 30 0 0 20.136s 100%
org.broadinstitute.hellbender.tools.spark.pipelines 309 1 18 1m40.75s 99%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics 25 0 0 3.612s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration 12 0 4 13.617s 100%
org.broadinstitute.hellbender.tools.spark.validation 6 0 0 3.590s 100%
org.broadinstitute.hellbender.tools.sv 25 0 0 1.796s 100%
org.broadinstitute.hellbender.tools.validation 6 0 0 0.715s 100%
org.broadinstitute.hellbender.tools.walkers 199 0 0 1m22.82s 100%
org.broadinstitute.hellbender.tools.walkers.annotator 34 0 0 18.643s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr 53 0 0 2m31.40s 100%
org.broadinstitute.hellbender.tools.walkers.consensus 2 0 0 0.787s 100%
org.broadinstitute.hellbender.tools.walkers.contamination 15 0 0 11.409s 100%
org.broadinstitute.hellbender.tools.walkers.conversion 9 0 0 0.963s 100%
org.broadinstitute.hellbender.tools.walkers.coverage 8 0 0 38.444s 100%
org.broadinstitute.hellbender.tools.walkers.fasta 28 0 0 2.584s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping 13 0 0 59.157s 100%
org.broadinstitute.hellbender.tools.walkers.filters 30 0 0 2.913s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth 14 0 0 11.988s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller 3 0 0 2.371s 100%
org.broadinstitute.hellbender.tools.walkers.mutect 2 0 0 6.047s 100%
org.broadinstitute.hellbender.tools.walkers.qc 13 0 0 1.359s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation 7 0 0 39.503s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter 1 0 0 2.300s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq 32 0 0 35.416s 100%
org.broadinstitute.hellbender.tools.walkers.sv 38 0 0 35.952s 100%
org.broadinstitute.hellbender.tools.walkers.validation 31 0 0 3.399s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup 2 0 0 0.947s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval 46 0 0 17.664s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling 2 0 0 0.765s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils 195 0 0 31.155s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr 29 0 0 36.134s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable 11 0 0 1.269s 100%
org.broadinstitute.hellbender.utils.config 3 0 0 0.440s 100%
org.broadinstitute.hellbender.utils.help 4 0 0 0.001s 100%
org.broadinstitute.hellbender.utils.python 1 0 1 0s -
org.broadinstitute.hellbender.utils.read 1 0 0 0.057s 100%

Classes

Class Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender.BwaMemIntegrationTest 2 0 0 0.287s 100%
org.broadinstitute.hellbender.IntelInflaterDeflaterIntegrationTest 6 0 0 1.909s 100%
org.broadinstitute.hellbender.PrintFileDiagnosticsIntegrationTest 3 0 0 0.330s 100%
org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidatorIntegrationTest 2 0 0 0.179s 100%
org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest 3 0 0 0.032s 100%
org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutorIntegrationTest 2 0 0 0.169s 100%
org.broadinstitute.hellbender.engine.BundleSupportIntegrationTest 1 0 0 0.009s 100%
org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest 45 0 0 1m16.11s 100%
org.broadinstitute.hellbender.engine.FeatureSupportIntegrationTest 6 0 0 0.594s 100%
org.broadinstitute.hellbender.engine.GatkToolIntegrationTest 22 0 0 2.087s 100%
org.broadinstitute.hellbender.engine.GenomicsDBIntegrationTest 7 0 0 1.962s 100%
org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest 16 0 1 0.332s 100%
org.broadinstitute.hellbender.engine.PartialReadWalkerIntegrationTest 2 0 0 0.096s 100%
org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest 1 0 0 2.871s 100%
org.broadinstitute.hellbender.engine.ReadWalkerIntegrationTest 2 0 0 0.175s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationSparkIntegrationTest 3 0 0 2.838s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationWalkerIntegrationTest 3 0 0 0.410s 100%
org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest 7 0 0 0.356s 100%
org.broadinstitute.hellbender.engine.WalkerOutputIntegrationTest 1 0 0 0.096s 100%
org.broadinstitute.hellbender.engine.filters.flow.WellFormedFlowBasedReadFilterIntegrationTest 2 0 0 0.413s 100%
org.broadinstitute.hellbender.engine.spark.GATKSparkToolIntegrationTest 1 0 0 0.106s 100%
org.broadinstitute.hellbender.tools.AddOriginalAlignmentTagsIntegrationTest 2 0 0 0.295s 100%
org.broadinstitute.hellbender.tools.BwaMemIndexImageCreatorIntegrationTest 1 0 0 2m4.83s 100%
org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotationsIntegrationTest 2 0 0 0.202s 100%
org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest 17 0 0 1.907s 100%
org.broadinstitute.hellbender.tools.CompareIntervalListsIntegrationTest 10 0 0 0.840s 100%
org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBamIntegrationTest 1 0 0 0.084s 100%
org.broadinstitute.hellbender.tools.CountBasesIntegrationTest 6 0 0 0.551s 100%
org.broadinstitute.hellbender.tools.CountReadsIntegrationTest 38 0 0 3.508s 100%
org.broadinstitute.hellbender.tools.CountVariantsIntegrationTest 10 0 0 7.388s 100%
org.broadinstitute.hellbender.tools.CreateBundleIntegrationTest 31 0 0 3.077s 100%
org.broadinstitute.hellbender.tools.DumpTabixIndexIntegrationTest 1 0 0 0.094s 100%
org.broadinstitute.hellbender.tools.FlagStatIntegrationTest 6 0 0 0.396s 100%
org.broadinstitute.hellbender.tools.GatherVcfsCloudIntegrationTest 12 0 0 1.300s 100%
org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest 3 0 0 0.296s 100%
org.broadinstitute.hellbender.tools.HtsgetReaderIntegrationTest 3 0 0 1.492s 100%
org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest 25 0 0 2.318s 100%
org.broadinstitute.hellbender.tools.LeftAlignIndelsIntegrationTest 1 0 0 0.160s 100%
org.broadinstitute.hellbender.tools.PrintBGZFBlockInformationIntegrationTest 8 0 0 0.701s 100%
org.broadinstitute.hellbender.tools.PrintReadsHeaderIntegrationTest 1 0 0 0.098s 100%
org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest 149 0 0 17.257s 100%
org.broadinstitute.hellbender.tools.SplitCRAMIntegrationTest 2 0 0 0.085s 100%
org.broadinstitute.hellbender.tools.SplitReadsIntegrationTest 35 0 0 4.809s 100%
org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervalsIntegrationTest 9 0 0 1.038s 100%
org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegmentsIntegrationTest 1 0 0 0.101s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsIntegrationTest 4 0 0 0.503s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest 4 0 0 2.572s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectReadCountsIntegrationTest 6 0 0 0.734s 100%
org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormalsIntegrationTest 36 0 0 11.125s 100%
org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest 48 0 0 4.127s 100%
org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest 1 0 0 0.076s 100%
org.broadinstitute.hellbender.tools.copynumber.FilterIntervalsIntegrationTest 30 0 0 2.887s 100%
org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCallerIntegrationTest 2 0 0 0.091s 100%
org.broadinstitute.hellbender.tools.copynumber.ModelSegmentsIntegrationTest 33 0 0 44.189s 100%
org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCallsIntegrationTest 1 0 0 0.088s 100%
org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervalsIntegrationTest 12 0 0 1.441s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatiosIntegrationTest 8 0 0 0.672s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegmentsIntegrationTest 14 0 0 1.175s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpointsIntegrationTest 15 0 0 1.415s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotationIntegrationTest 1 0 0 0.088s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsIntegrationTest 2 0 0 0.176s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEventsIntegrationTest 5 0 0 0.457s 100%
org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModelIntegrationTest 12 0 0 2m28.67s 100%
org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFileIntegrationTest 3 0 0 1m5.19s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerIntegrationTest 1 0 0 1.197s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest 2 0 0 2.905s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectMultiMetricsIntegrationTest 2 0 0 0.665s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectSingleMetricsIntegrationTest 1 0 0 0.219s 100%
org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalkerIntegrationTest 2 0 0 0.211s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerIntegrationTest 1 0 0 0.100s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSparkIntegrationTest 1 0 0 0.416s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerIntegrationTest 1 0 0 0.104s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSparkIntegrationTest 1 0 0 0.415s 100%
org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalkerIntegrationTest 8 0 0 0.229s 100%
org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutorIntegrationTest 2 0 0 0.216s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceIntegrationTest 2 0 0 0.186s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSparkIntegrationTest 1 0 0 0.272s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsIntegrationTest 1 0 0 0.092s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSparkIntegrationTest 1 0 0 0.264s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest 1 0 0 0.031s 100%
org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutorIntegrationTest 1 0 0 0.096s 100%
org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalkerIntegrationTest 1 0 0 0.100s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerIntegrationTest 1 0 0 0.099s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSparkIntegrationTest 1 0 0 0.234s 100%
org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsIntegrationTest 18 0 0 1.735s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotateSegmentsIntegrationTest 6 0 0 14.668s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest 58 0 0 1m37.70s 100%
org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibilityIntegrationTest 16 0 0 1.491s 100%
org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest 23 0 0 2.916s 100%
org.broadinstitute.hellbender.tools.spark.ApplyBQSRSparkIntegrationTest 9 0 0 5.090s 100%
org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest 11 0 0 1m14.13s 100%
org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndexIntegrationTest 10 0 0 0.893s 100%
org.broadinstitute.hellbender.tools.spark.PileupSparkIntegrationTest 10 0 2 3.846s 100%
org.broadinstitute.hellbender.tools.spark.RevertSamSparkIntegrationTest 27 0 0 9.407s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaAndMarkDuplicatesPipelineSparkIntegrationTest 1 0 0 1.583s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkIntegrationTest 2 0 0 1.034s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmersSparkIntegrationTest 12 0 0 1.061s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomyIntegrationTest 5 0 0 0.415s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSparkIntegrationTest 1 0 0 1.404s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSparkIntegrationTest 6 0 0 9.019s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest 2 0 0 3.415s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreIntegrationTest 4 0 0 4.822s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest 3 0 0 5.183s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSparkIntegrationTest 7 0 0 1.699s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest 19 0 0 3.978s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSparkIntegrationTest 16 0 0 5.535s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSparkIntegrationTest 4 0 0 0.810s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest 152 0 0 1m0.10s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest 95 1 18 20.551s 98%
org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSparkIntegrationTest 13 0 0 2.899s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSparkIntegrationTest 2 0 0 0.091s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSparkIntegrationTest 6 0 0 1.028s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest 8 0 0 1.155s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSparkIntegrationTest 7 0 0 1.253s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSparkIntegrationTest 2 0 0 0.085s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.CpxVariantReInterpreterSparkIntegrationTest 2 0 1 1.320s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest 2 0 1 0.357s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest 2 0 0 0.814s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.FindBreakpointEvidenceSparkIntegrationTest 2 0 1 2.601s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.StructuralVariationDiscoveryPipelineSparkIntegrationTest 2 0 1 3.066s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest 2 0 0 5.459s 100%
org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest 6 0 0 3.590s 100%
org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidenceIntegrationTest 2 0 0 0.211s 100%
org.broadinstitute.hellbender.tools.sv.PrintReadCountsIntegrationTest 3 0 0 0.345s 100%
org.broadinstitute.hellbender.tools.sv.PrintSVEvidenceIntegrationTest 16 0 0 0.877s 100%
org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAFIntegrationTest 4 0 0 0.363s 100%
org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest 6 0 0 0.715s 100%
org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest 29 0 0 11.351s 100%
org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsIntegrationTest 98 0 0 52.277s 100%
org.broadinstitute.hellbender.tools.walkers.GnarlyGenotyperIntegrationTest 16 0 0 11.080s 100%
org.broadinstitute.hellbender.tools.walkers.MethylationTypeCallerIntegrationTest 1 0 0 0.129s 100%
org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest 4 0 0 1.921s 100%
org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScoresIntegrationTest 3 0 0 0.407s 100%
org.broadinstitute.hellbender.tools.walkers.SplitIntervalsIntegrationTest 9 0 0 1.754s 100%
org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicatesIntegrationTest 2 0 0 0.174s 100%
org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest 37 0 0 3.724s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.DirichletAlleleDepthAndFractionIntegrationTest 26 0 0 14.462s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorIntegrationTest 8 0 0 4.181s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariatesIntegrationTest 5 0 0 1.004s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSRIntegrationTest 24 0 0 10.364s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest 21 0 0 1m1.66s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest 1 0 0 55.546s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReportsIntegrationTest 2 0 0 22.823s 100%
org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSetIntegrationTest 2 0 0 0.787s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContaminationIntegrationTest 11 0 0 7.786s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummariesIntegrationTest 2 0 0 2.504s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummariesIntegrationTest 2 0 0 1.119s 100%
org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBedIntegrationTest 9 0 0 0.963s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.CallableLociIntegrationTest 1 0 0 15.750s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageIntegrationTest 7 0 0 22.694s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest 3 0 0 0.078s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest 17 0 0 1.639s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMakerIntegrationTest 6 0 0 0.603s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFastaIntegrationTest 2 0 0 0.264s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest 3 0 0 1.598s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperIntegrationTest 7 0 0 55.773s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypesIntegrationTest 3 0 0 1.786s 100%
org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltrationIntegrationTest 30 0 0 2.913s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQualityIntegrationTest 4 0 0 0.233s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilderIntegrationTest 3 0 0 10.466s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorerIntegrationTest 7 0 0 1.289s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentIntegrationTest 2 0 0 2.347s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHaplotypeIntegrationTest 1 0 0 0.024s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactDataIntegrationTest 1 0 0 5.942s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStatsIntegrationTest 1 0 0 0.105s 100%
org.broadinstitute.hellbender.tools.walkers.qc.CheckPileupIntegrationTest 2 0 0 0.217s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PileupIntegrationTest 5 0 0 0.461s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEMIntegrationTest 1 0 0 0.139s 100%
org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTagsIntegrationTest 5 0 0 0.542s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsIntegrationTest 3 0 0 0.867s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelIntegrationTest 4 0 0 38.636s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifactsIntegrationTest 1 0 0 2.300s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounterIntegrationTest 12 0 0 5.352s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluationIntegrationTest 11 0 0 14.967s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReadsIntegrationTest 9 0 0 15.097s 100%
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidenceIntegrationTest 4 0 0 6.135s 100%
org.broadinstitute.hellbender.tools.walkers.sv.GroupedSVClusterIntegrationTest 1 0 0 1.013s 100%
org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentationIntegrationTest 3 0 0 0.799s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest 6 0 0 2.238s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVClusterIntegrationTest 10 0 0 8.796s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVConcordanceIntegrationTest 9 0 0 16.083s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVStratifyIntegrationTest 5 0 0 0.888s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepthIntegrationTest 1 0 0 0.135s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFractionIntegrationTest 1 0 0 0.123s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractionsIntegrationTest 1 0 0 0.175s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceIntegrationTest 6 0 0 0.704s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositivesIntegrationTest 2 0 0 0.289s 100%
org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordanceIntegrationTest 2 0 0 0.207s 100%
org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3IntegrationTest 1 0 0 0.115s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordanceIntegrationTest 16 0 0 1.556s 100%
org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndelsIntegrationTest 1 0 0 0.095s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest 2 0 0 0.947s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQCIntegrationTest 1 0 0 0.150s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest 45 0 0 17.514s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerIntegrationTest 2 0 0 0.765s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriorsIntegrationTest 14 0 0 2.186s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest 9 0 0 0.881s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest 32 0 0 13.176s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest 88 0 0 8.001s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionaryIntegrationTest 14 0 0 1.208s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest 17 0 0 3.684s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTableIntegrationTest 21 0 0 2.019s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSRIntegrationTest 7 0 0 3.082s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranchesIntegrationTest 4 0 0 0.313s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.NVScoreVariantsIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorIntegrationTest 17 0 0 32.668s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest 5 0 0 0.754s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotationsIntegrationTest 3 0 0 0.347s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest 3 0 0 0.168s 100%
org.broadinstitute.hellbender.utils.config.ConfigIntegrationTest 2 0 0 0.178s 100%
org.broadinstitute.hellbender.utils.config.ConfigPrintReadsIntegrationTest 1 0 0 0.262s 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 0.001s 100%
org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest 1 0 1 0s -
org.broadinstitute.hellbender.utils.read.FlowBasedReadIntegrationTest 1 0 0 0.057s 100%