Test Summary

2211

tests
1

failures
17

ignored
24m2.35s

duration
99%

successful

Ignored tests

Packages

Package Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender 11 0 0 2.162s 100%
org.broadinstitute.hellbender.cmdline 7 0 0 0.344s 100%
org.broadinstitute.hellbender.engine 117 0 0 1m36.12s 100%
org.broadinstitute.hellbender.engine.filters.flow 2 0 0 0.462s 100%
org.broadinstitute.hellbender.engine.spark 1 0 0 0.076s 100%
org.broadinstitute.hellbender.tools 364 0 0 2m50.60s 100%
org.broadinstitute.hellbender.tools.copynumber 187 0 0 1m4.00s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting 22 0 0 1.449s 100%
org.broadinstitute.hellbender.tools.copynumber.utils 23 0 0 1.584s 100%
org.broadinstitute.hellbender.tools.dragstr 15 0 0 2m59.19s 100%
org.broadinstitute.hellbender.tools.examples 32 0 0 7.147s 100%
org.broadinstitute.hellbender.tools.funcotator 82 0 0 1m59.43s 100%
org.broadinstitute.hellbender.tools.reference 39 0 0 3.177s 100%
org.broadinstitute.hellbender.tools.spark 67 0 0 1m16.14s 100%
org.broadinstitute.hellbender.tools.spark.bwa 3 0 0 2.580s 100%
org.broadinstitute.hellbender.tools.spark.pathseq 30 0 0 19.839s 100%
org.broadinstitute.hellbender.tools.spark.pipelines 309 1 17 1m42.40s 99%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics 25 0 0 3.184s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration 12 0 0 36.338s 100%
org.broadinstitute.hellbender.tools.spark.validation 6 0 0 3.319s 100%
org.broadinstitute.hellbender.tools.sv 25 0 0 1.281s 100%
org.broadinstitute.hellbender.tools.validation 6 0 0 0.620s 100%
org.broadinstitute.hellbender.tools.walkers 199 0 0 1m16.01s 100%
org.broadinstitute.hellbender.tools.walkers.annotator 34 0 0 17.339s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr 53 0 0 1m55.99s 100%
org.broadinstitute.hellbender.tools.walkers.consensus 2 0 0 0.789s 100%
org.broadinstitute.hellbender.tools.walkers.contamination 15 0 0 10.768s 100%
org.broadinstitute.hellbender.tools.walkers.conversion 9 0 0 0.734s 100%
org.broadinstitute.hellbender.tools.walkers.coverage 8 0 0 38.230s 100%
org.broadinstitute.hellbender.tools.walkers.fasta 28 0 0 2.034s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping 13 0 0 57.797s 100%
org.broadinstitute.hellbender.tools.walkers.filters 30 0 0 2.211s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth 14 0 0 11.237s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller 3 0 0 2.029s 100%
org.broadinstitute.hellbender.tools.walkers.mutect 2 0 0 5.759s 100%
org.broadinstitute.hellbender.tools.walkers.qc 13 0 0 0.978s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation 7 0 0 40.188s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter 1 0 0 2.172s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq 32 0 0 33.386s 100%
org.broadinstitute.hellbender.tools.walkers.sv 38 0 0 36.141s 100%
org.broadinstitute.hellbender.tools.walkers.validation 31 0 0 2.956s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup 2 0 0 0.760s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval 46 0 0 16.238s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling 2 0 0 0.981s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils 195 0 0 25.410s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr 29 0 0 34.758s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable 11 0 0 0.996s 100%
org.broadinstitute.hellbender.utils.config 3 0 0 0.413s 100%
org.broadinstitute.hellbender.utils.help 4 0 0 14.388s 100%
org.broadinstitute.hellbender.utils.python 1 0 0 0.165s 100%
org.broadinstitute.hellbender.utils.read 1 0 0 0.054s 100%

Classes

Class Tests Failures Ignored Duration Success rate
org.broadinstitute.hellbender.BwaMemIntegrationTest 2 0 0 0.239s 100%
org.broadinstitute.hellbender.IntelInflaterDeflaterIntegrationTest 6 0 0 1.604s 100%
org.broadinstitute.hellbender.PrintFileDiagnosticsIntegrationTest 3 0 0 0.319s 100%
org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidatorIntegrationTest 2 0 0 0.163s 100%
org.broadinstitute.hellbender.cmdline.CommandLineProgramIntegrationTest 3 0 0 0.037s 100%
org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutorIntegrationTest 2 0 0 0.144s 100%
org.broadinstitute.hellbender.engine.BundleSupportIntegrationTest 1 0 0 0.011s 100%
org.broadinstitute.hellbender.engine.CRAMSupportIntegrationTest 45 0 0 1m20.46s 100%
org.broadinstitute.hellbender.engine.FeatureSupportIntegrationTest 6 0 0 0.500s 100%
org.broadinstitute.hellbender.engine.GatkToolIntegrationTest 22 0 0 1.761s 100%
org.broadinstitute.hellbender.engine.GenomicsDBIntegrationTest 7 0 0 1.681s 100%
org.broadinstitute.hellbender.engine.MultiVariantWalkerIntegrationTest 17 0 0 4.309s 100%
org.broadinstitute.hellbender.engine.PartialReadWalkerIntegrationTest 2 0 0 0.075s 100%
org.broadinstitute.hellbender.engine.PipelineSupportIntegrationTest 1 0 0 3.268s 100%
org.broadinstitute.hellbender.engine.ReadWalkerIntegrationTest 2 0 0 0.184s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationSparkIntegrationTest 3 0 0 3.124s 100%
org.broadinstitute.hellbender.engine.SequenceDictionaryValidationWalkerIntegrationTest 3 0 0 0.338s 100%
org.broadinstitute.hellbender.engine.VariantWalkerIntegrationTest 7 0 0 0.328s 100%
org.broadinstitute.hellbender.engine.WalkerOutputIntegrationTest 1 0 0 0.082s 100%
org.broadinstitute.hellbender.engine.filters.flow.WellFormedFlowBasedReadFilterIntegrationTest 2 0 0 0.462s 100%
org.broadinstitute.hellbender.engine.spark.GATKSparkToolIntegrationTest 1 0 0 0.076s 100%
org.broadinstitute.hellbender.tools.AddOriginalAlignmentTagsIntegrationTest 2 0 0 0.252s 100%
org.broadinstitute.hellbender.tools.BwaMemIndexImageCreatorIntegrationTest 1 0 0 2m4.72s 100%
org.broadinstitute.hellbender.tools.CalculateAverageCombinedAnnotationsIntegrationTest 2 0 0 0.149s 100%
org.broadinstitute.hellbender.tools.ClipReadsIntegrationTest 17 0 0 1.469s 100%
org.broadinstitute.hellbender.tools.CompareIntervalListsIntegrationTest 10 0 0 0.599s 100%
org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBamIntegrationTest 1 0 0 0.058s 100%
org.broadinstitute.hellbender.tools.CountBasesIntegrationTest 6 0 0 0.353s 100%
org.broadinstitute.hellbender.tools.CountReadsIntegrationTest 38 0 0 2.349s 100%
org.broadinstitute.hellbender.tools.CountVariantsIntegrationTest 10 0 0 7.360s 100%
org.broadinstitute.hellbender.tools.CreateBundleIntegrationTest 31 0 0 1.830s 100%
org.broadinstitute.hellbender.tools.DumpTabixIndexIntegrationTest 1 0 0 0.061s 100%
org.broadinstitute.hellbender.tools.FlagStatIntegrationTest 6 0 0 0.243s 100%
org.broadinstitute.hellbender.tools.GatherVcfsCloudIntegrationTest 12 0 0 0.941s 100%
org.broadinstitute.hellbender.tools.GetSampleNameIntegrationTest 3 0 0 0.196s 100%
org.broadinstitute.hellbender.tools.HtsgetReaderIntegrationTest 3 0 0 9.524s 100%
org.broadinstitute.hellbender.tools.IndexFeatureFileIntegrationTest 25 0 0 1.748s 100%
org.broadinstitute.hellbender.tools.LeftAlignIndelsIntegrationTest 1 0 0 0.126s 100%
org.broadinstitute.hellbender.tools.PrintBGZFBlockInformationIntegrationTest 8 0 0 0.504s 100%
org.broadinstitute.hellbender.tools.PrintReadsHeaderIntegrationTest 1 0 0 0.063s 100%
org.broadinstitute.hellbender.tools.PrintReadsIntegrationTest 149 0 0 14.247s 100%
org.broadinstitute.hellbender.tools.SplitCRAMIntegrationTest 2 0 0 0.060s 100%
org.broadinstitute.hellbender.tools.SplitReadsIntegrationTest 35 0 0 3.746s 100%
org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervalsIntegrationTest 9 0 0 0.728s 100%
org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegmentsIntegrationTest 1 0 0 0.112s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsIntegrationTest 4 0 0 0.353s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSparkIntegrationTest 4 0 0 2.520s 100%
org.broadinstitute.hellbender.tools.copynumber.CollectReadCountsIntegrationTest 6 0 0 0.454s 100%
org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormalsIntegrationTest 36 0 0 10.004s 100%
org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest 48 0 0 2.791s 100%
org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidyIntegrationTest 1 0 0 0.060s 100%
org.broadinstitute.hellbender.tools.copynumber.FilterIntervalsIntegrationTest 30 0 0 2.194s 100%
org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCallerIntegrationTest 2 0 0 0.066s 100%
org.broadinstitute.hellbender.tools.copynumber.ModelSegmentsIntegrationTest 33 0 0 43.559s 100%
org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCallsIntegrationTest 1 0 0 0.065s 100%
org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervalsIntegrationTest 12 0 0 1.093s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatiosIntegrationTest 8 0 0 0.544s 100%
org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegmentsIntegrationTest 14 0 0 0.905s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpointsIntegrationTest 15 0 0 1.036s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotationIntegrationTest 1 0 0 0.070s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsIntegrationTest 2 0 0 0.130s 100%
org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEventsIntegrationTest 5 0 0 0.348s 100%
org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModelIntegrationTest 12 0 0 1m51.95s 100%
org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFileIntegrationTest 3 0 0 1m7.23s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerIntegrationTest 1 0 0 0.950s 100%
org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSparkIntegrationTest 2 0 0 2.812s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectMultiMetricsIntegrationTest 2 0 0 0.636s 100%
org.broadinstitute.hellbender.tools.examples.ExampleCollectSingleMetricsIntegrationTest 1 0 0 0.189s 100%
org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalkerIntegrationTest 2 0 0 0.140s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerIntegrationTest 1 0 0 0.068s 100%
org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSparkIntegrationTest 1 0 0 0.390s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerIntegrationTest 1 0 0 0.091s 100%
org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSparkIntegrationTest 1 0 0 0.398s 100%
org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalkerIntegrationTest 8 0 0 0.134s 100%
org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutorIntegrationTest 2 0 0 0.158s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceIntegrationTest 2 0 0 0.133s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSparkIntegrationTest 1 0 0 0.246s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSparkIntegrationTest 1 0 0 0.269s 100%
org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalkerIntegrationTest 1 0 0 0.016s 100%
org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutorIntegrationTest 1 0 0 0.071s 100%
org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalkerIntegrationTest 1 0 0 0.077s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerIntegrationTest 1 0 0 0.073s 100%
org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSparkIntegrationTest 1 0 0 0.225s 100%
org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsIntegrationTest 18 0 0 1.318s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotateSegmentsIntegrationTest 6 0 0 13.740s 100%
org.broadinstitute.hellbender.tools.funcotator.FuncotatorIntegrationTest 58 0 0 1m44.37s 100%
org.broadinstitute.hellbender.tools.reference.CheckReferenceCompatibilityIntegrationTest 16 0 0 1.012s 100%
org.broadinstitute.hellbender.tools.reference.CompareReferencesIntegrationTest 23 0 0 2.165s 100%
org.broadinstitute.hellbender.tools.spark.ApplyBQSRSparkIntegrationTest 9 0 0 5.020s 100%
org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSparkIntegrationTest 11 0 0 53.832s 100%
org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndexIntegrationTest 10 0 0 0.683s 100%
org.broadinstitute.hellbender.tools.spark.PileupSparkIntegrationTest 10 0 0 7.004s 100%
org.broadinstitute.hellbender.tools.spark.RevertSamSparkIntegrationTest 27 0 0 9.605s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaAndMarkDuplicatesPipelineSparkIntegrationTest 1 0 0 1.578s 100%
org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkIntegrationTest 2 0 0 1.002s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmersSparkIntegrationTest 12 0 0 0.935s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomyIntegrationTest 5 0 0 0.373s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSparkIntegrationTest 1 0 0 1.363s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSparkIntegrationTest 6 0 0 8.931s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSparkIntegrationTest 2 0 0 3.427s 100%
org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreIntegrationTest 4 0 0 4.810s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSparkIntegrationTest 3 0 0 5.270s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSparkIntegrationTest 7 0 0 1.456s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSparkIntegrationTest 19 0 0 3.534s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSparkIntegrationTest 16 0 0 5.228s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSparkIntegrationTest 4 0 0 0.719s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.MarkDuplicatesSparkIntegrationTest 152 0 0 59.001s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSparkIntegrationTest 95 1 17 24.400s 98%
org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSparkIntegrationTest 13 0 0 2.794s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSparkIntegrationTest 2 0 0 0.064s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSparkIntegrationTest 6 0 0 0.943s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest 8 0 0 0.996s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSparkIntegrationTest 7 0 0 1.118s 100%
org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSparkIntegrationTest 2 0 0 0.063s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.CpxVariantReInterpreterSparkIntegrationTest 2 0 0 7.810s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.DiscoverVariantsFromContigAlignmentsSAMSparkIntegrationTest 2 0 0 2.096s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.ExtractOriginalAlignmentRecordsByNameSparkIntegrationTest 2 0 0 0.877s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.FindBreakpointEvidenceSparkIntegrationTest 2 0 0 7.132s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.StructuralVariationDiscoveryPipelineSparkIntegrationTest 2 0 0 13.074s 100%
org.broadinstitute.hellbender.tools.spark.sv.integration.SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest 2 0 0 5.349s 100%
org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest 6 0 0 3.319s 100%
org.broadinstitute.hellbender.tools.sv.CondenseDepthEvidenceIntegrationTest 2 0 0 0.204s 100%
org.broadinstitute.hellbender.tools.sv.PrintReadCountsIntegrationTest 3 0 0 0.213s 100%
org.broadinstitute.hellbender.tools.sv.PrintSVEvidenceIntegrationTest 16 0 0 0.613s 100%
org.broadinstitute.hellbender.tools.sv.SiteDepthtoBAFIntegrationTest 4 0 0 0.251s 100%
org.broadinstitute.hellbender.tools.validation.CompareBaseQualitiesIntegrationTest 6 0 0 0.620s 100%
org.broadinstitute.hellbender.tools.walkers.CombineGVCFsIntegrationTest 29 0 0 10.236s 100%
org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsIntegrationTest 98 0 0 49.011s 100%
org.broadinstitute.hellbender.tools.walkers.GnarlyGenotyperIntegrationTest 16 0 0 10.050s 100%
org.broadinstitute.hellbender.tools.walkers.MethylationTypeCallerIntegrationTest 1 0 0 0.107s 100%
org.broadinstitute.hellbender.tools.walkers.ReadAnonymizerIntegrationTest 4 0 0 1.654s 100%
org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScoresIntegrationTest 3 0 0 0.282s 100%
org.broadinstitute.hellbender.tools.walkers.SplitIntervalsIntegrationTest 9 0 0 1.623s 100%
org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicatesIntegrationTest 2 0 0 0.189s 100%
org.broadinstitute.hellbender.tools.walkers.ValidateVariantsIntegrationTest 37 0 0 2.858s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.DirichletAlleleDepthAndFractionIntegrationTest 26 0 0 12.884s 100%
org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorIntegrationTest 8 0 0 4.455s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariatesIntegrationTest 5 0 0 1.044s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSRIntegrationTest 24 0 0 11.686s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest 21 0 0 43.266s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest 1 0 0 43.468s 100%
org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReportsIntegrationTest 2 0 0 16.524s 100%
org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSetIntegrationTest 2 0 0 0.789s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContaminationIntegrationTest 11 0 0 7.793s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummariesIntegrationTest 2 0 0 1.943s 100%
org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummariesIntegrationTest 2 0 0 1.032s 100%
org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBedIntegrationTest 9 0 0 0.734s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.CallableLociIntegrationTest 1 0 0 14.757s 100%
org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageIntegrationTest 7 0 0 23.473s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReferenceIntegrationTest 3 0 0 0.051s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMakerIntegrationTest 17 0 0 1.304s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMakerIntegrationTest 6 0 0 0.470s 100%
org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFastaIntegrationTest 2 0 0 0.209s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityIntegrationTest 3 0 0 1.410s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperIntegrationTest 7 0 0 54.646s 100%
org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypesIntegrationTest 3 0 0 1.741s 100%
org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltrationIntegrationTest 30 0 0 2.211s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQualityIntegrationTest 4 0 0 0.210s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilderIntegrationTest 3 0 0 9.909s 100%
org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorerIntegrationTest 7 0 0 1.118s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentIntegrationTest 2 0 0 2.005s 100%
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHaplotypeIntegrationTest 1 0 0 0.024s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactDataIntegrationTest 1 0 0 5.695s 100%
org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStatsIntegrationTest 1 0 0 0.064s 100%
org.broadinstitute.hellbender.tools.walkers.qc.CheckPileupIntegrationTest 2 0 0 0.165s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PileupIntegrationTest 5 0 0 0.310s 100%
org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEMIntegrationTest 1 0 0 0.110s 100%
org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTagsIntegrationTest 5 0 0 0.393s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsIntegrationTest 3 0 0 0.613s 100%
org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelIntegrationTest 4 0 0 39.575s 100%
org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifactsIntegrationTest 1 0 0 2.172s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounterIntegrationTest 12 0 0 5.124s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluationIntegrationTest 11 0 0 13.841s 100%
org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReadsIntegrationTest 9 0 0 14.421s 100%
org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidenceIntegrationTest 4 0 0 6.080s 100%
org.broadinstitute.hellbender.tools.walkers.sv.GroupedSVClusterIntegrationTest 1 0 0 1.022s 100%
org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentationIntegrationTest 3 0 0 0.616s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVAnnotateIntegrationTest 6 0 0 2.195s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVClusterIntegrationTest 10 0 0 9.196s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVConcordanceIntegrationTest 9 0 0 16.311s 100%
org.broadinstitute.hellbender.tools.walkers.sv.SVStratifyIntegrationTest 5 0 0 0.721s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepthIntegrationTest 1 0 0 0.102s 100%
org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFractionIntegrationTest 1 0 0 0.096s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractionsIntegrationTest 1 0 0 0.160s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceIntegrationTest 6 0 0 0.671s 100%
org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositivesIntegrationTest 2 0 0 0.244s 100%
org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordanceIntegrationTest 2 0 0 0.181s 100%
org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3IntegrationTest 1 0 0 0.122s 100%
org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordanceIntegrationTest 16 0 0 1.313s 100%
org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndelsIntegrationTest 1 0 0 0.067s 100%
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutationsIntegrationTest 2 0 0 0.760s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQCIntegrationTest 1 0 0 0.134s 100%
org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalIntegrationTest 45 0 0 16.104s 100%
org.broadinstitute.hellbender.tools.walkers.variantrecalling.HaplotypeBasedVariantRecallerIntegrationTest 2 0 0 0.981s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriorsIntegrationTest 14 0 0 1.882s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariantsIntegrationTest 9 0 0 0.720s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCFIntegrationTest 32 0 0 11.863s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariantsIntegrationTest 88 0 0 5.722s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionaryIntegrationTest 14 0 0 0.843s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VCFComparatorIntegrationTest 17 0 0 2.982s 100%
org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTableIntegrationTest 21 0 0 1.398s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSRIntegrationTest 7 0 0 2.728s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranchesIntegrationTest 4 0 0 0.240s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.NVScoreVariantsIntegrationTest 1 0 0 0.055s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorIntegrationTest 17 0 0 31.735s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ExtractVariantAnnotationsIntegrationTest 5 0 0 0.634s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotationsIntegrationTest 3 0 0 0.230s 100%
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModelIntegrationTest 3 0 0 0.132s 100%
org.broadinstitute.hellbender.utils.config.ConfigIntegrationTest 2 0 0 0.139s 100%
org.broadinstitute.hellbender.utils.config.ConfigPrintReadsIntegrationTest 1 0 0 0.274s 100%
org.broadinstitute.hellbender.utils.help.DocumentationGenerationIntegrationTest 1 0 0 5.289s 100%
org.broadinstitute.hellbender.utils.help.TabCompletionIntegrationTest 1 0 0 5.179s 100%
org.broadinstitute.hellbender.utils.help.WDLGenerationIntegrationTest 2 0 0 3.920s 100%
org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest 1 0 0 0.165s 100%
org.broadinstitute.hellbender.utils.read.FlowBasedReadIntegrationTest 1 0 0 0.054s 100%