Download gatk.jar - @org.broadinstitute

Version	Vulnerabilities	Size	Updated
4.4.x	gatk-4.4.0.0.jar		48.63 MB	Mar 16, 2023
4.3.x	gatk-4.3.0.0.jar		48.56 MB	Oct 13, 2022
4.2.x	gatk-4.2.6.1.jar		45.40 MB	Apr 13, 2022
gatk-4.2.6.0.jar		45.40 MB	Apr 08, 2022
gatk-4.2.5.0.jar		45.32 MB	Feb 04, 2022
gatk-4.2.4.1.jar		45.30 MB	Jan 04, 2022
gatk-4.2.4.0.jar		45.30 MB	Dec 15, 2021
gatk-4.2.3.0.jar		45.30 MB	Nov 02, 2021
gatk-4.2.2.0.jar		45.26 MB	Aug 19, 2021
gatk-4.2.1.0.jar		45.24 MB	Jul 30, 2021
gatk-4.2.0.0.jar		45.09 MB	Feb 19, 2021
4.1.x	gatk-4.1.9.0.jar		44.83 MB	Oct 10, 2020
gatk-4.1.8.1.jar		44.77 MB	Jul 20, 2020
gatk-4.1.8.0.jar		44.76 MB	Jun 26, 2020
gatk-4.1.7.0.jar		44.75 MB	Apr 23, 2020
gatk-4.1.6.0.jar		44.71 MB	Mar 25, 2020
gatk-4.1.5.0.jar		44.68 MB	Feb 28, 2020
gatk-4.1.4.1.jar		44.70 MB	Nov 27, 2019
gatk-4.1.4.0.jar		44.66 MB	Oct 16, 2019
gatk-4.1.3.0.jar		44.68 MB	Aug 09, 2019
gatk-4.1.2.0.jar		44.58 MB	Apr 23, 2019
gatk-4.1.1.0.jar		44.53 MB	Mar 29, 2019
gatk-4.1.0.0.jar		44.44 MB	Jan 30, 2019
4.0.x	gatk-4.0.12.0.jar		44.41 MB	Dec 17, 2018
gatk-4.0.11.0.jar		44.24 MB	Oct 23, 2018
gatk-4.0.10.1.jar		47.29 MB	Oct 09, 2018
gatk-4.0.10.0.jar		47.27 MB	Oct 03, 2018
gatk-4.0.9.0.jar		47.25 MB	Sep 25, 2018
gatk-4.0.8.1.jar		47.26 MB	Aug 16, 2018
gatk-4.0.8.0.jar		47.25 MB	Aug 15, 2018
gatk-4.0.7.0.jar		47.18 MB	Jul 30, 2018
gatk-4.0.6.0.jar		47.06 MB	Jul 06, 2018
gatk-4.0.5.2.jar		47.05 MB	Jun 29, 2018
gatk-4.0.5.1.jar		47.01 MB	Jun 11, 2018
gatk-4.0.5.0.jar		47 MB	Jun 07, 2018
gatk-4.0.4.0.jar		46.94 MB	Apr 26, 2018
gatk-4.0.3.0.jar		46.87 MB	Mar 27, 2018
gatk-4.0.2.1.jar		22.84 MB	Mar 02, 2018
gatk-4.0.2.0.jar		22.83 MB	Feb 27, 2018
gatk-4.0.1.2.jar		22.83 MB	Feb 09, 2018
gatk-4.0.1.1.jar		22.82 MB	Feb 01, 2018
gatk-4.0.1.0.jar		22.82 MB	Jan 30, 2018
gatk-4.0.0.0.jar		3.79 MB	Jan 09, 2018
4.beta.x	gatk-4.beta.2.jar		4.18 MB	Jul 20, 2017
gatk-4.beta.1.jar		4.09 MB	Jun 28, 2017
4.alpha.x	gatk-4.alpha.2.jar		2.21 MB	Aug 17, 2016
gatk-4.alpha.1.jar		2.03 MB	Apr 29, 2016
4.alpha	gatk-4.alpha.jar			Mar 03, 2016

View Java Class Source Code in JAR file

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org.broadinstitute.hellbender.utils.downsampling

├─ org.broadinstitute.hellbender.utils.downsampling.AlleleBiasedDownsamplingUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.DownsampleType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.Downsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.DownsamplingMethod.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.FractionalDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.LevelingDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.MutectDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.PassThroughDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.PositionalDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.ReadsDownsampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.ReadsDownsamplingIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.downsampling.ReservoirDownsampler.class - [JAR]

org.broadinstitute.hellbender.cmdline

├─ org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidator.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.CommandLineProgram.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.DeprecatedToolsRegistry.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.TestProgramGroup.class - [JAR]

org.broadinstitute.hellbender.tools.examples

├─ org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSpark.class - [JAR]

org.broadinstitute.hellbender.tools.spark.pipelines.metrics

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectBaseDistributionByCycleSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectInsertSizeMetricsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectMultipleMetricsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.InsertSizeMetricsCollectorSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MeanQualityByCycleSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityScoreDistributionSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.metrics.QualityYieldMetricsCollectorSpark.class - [JAR]

org.broadinstitute.hellbender.tools.sv.cluster

├─ org.broadinstitute.hellbender.tools.sv.cluster.BinnedCNVLinkage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.CNVLinkage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVCollapser.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.CanonicalSVLinkage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.ClusteringParameters.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.PloidyTable.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineArgumentsCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.SVClusterEngineFactory.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.SVClusterLinkage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.cluster.SVCollapser.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv.evidence

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidenceClusterer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.CalcMetadataSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceFeatures.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceOverlapChecker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLinkClusterer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.IntervalCoverageFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCleaner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCounter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameKmerizer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.QNamesForKmersFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadClassifier.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadsForQNamesFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.evidence.XGBoostEvidenceFilter.class - [JAR]

org.broadinstitute.hellbender.cmdline.argumentcollections

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.MetricAccumulationLevelArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalFeatureInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReadInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReferenceInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredFeatureInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReferenceInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredVariantInputArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.LocatableXsvFuncotationFactory.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory.class - [JAR]

org.broadinstitute.hellbender.tools.dragstr

├─ org.broadinstitute.hellbender.tools.dragstr.BufferedReferenceBases.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.CalibrateDragstrModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.ComposeSTRTableFile.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrHyperParameters.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrLocus.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCase.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrLocusCases.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrLocusUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.DragstrParametersEstimator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.InterleavingListSpliterator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.STRDecimationTable.class - [JAR]

├─ org.broadinstitute.hellbender.tools.dragstr.StratifiedDragstrLocusCases.class - [JAR]

org.broadinstitute.hellbender.cmdline.GATKPlugin

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor.class - [JAR]

org.broadinstitute.hellbender.utils.python

├─ org.broadinstitute.hellbender.utils.python.PythonExecutorBase.class - [JAR]

├─ org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException.class - [JAR]

├─ org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv.discovery.inference

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointComplications.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.BreakpointsInference.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ContigChimericAlignmentIterativeInterpreter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantCanonicalRepresentation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInducingAssemblyContig.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantInterpreter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantReInterpreterSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.CpxVariantType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.ImpreciseVariantDetector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.NovelAdjacencyAndAltHaplotype.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SegmentedCpxVariantSimpleVariantExtractor.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleChimera.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyAndChimericAlignmentEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.SimpleNovelAdjacencyInterpreter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.inference.TypeInferredFromSimpleChimera.class - [JAR]

org.broadinstitute.hellbender.utils.codecs

├─ org.broadinstitute.hellbender.utils.codecs.AbstractBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.BafEvidenceBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.BafEvidenceCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.DepthEvidenceBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.DepthEvidenceCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.DiscordantPairEvidenceCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.FeatureOutputCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.FeatureSink.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.FeaturesHeader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.LineIteratorReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.LocusDepthBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.LocusDepthCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceBCICodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.SplitReadEvidenceCodec.class - [JAR]

org.broadinstitute.hellbender.utils.collections

├─ org.broadinstitute.hellbender.utils.collections.AutoCloseableCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.HopscotchCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.HopscotchMap.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.HopscotchMultiMap.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.HopscotchSet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.HopscotchUniqueMultiMap.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.IndexedSet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.NestedIntegerArray.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.Permutation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.collections.SetSizeUtils.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.haplotypecaller

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrPairHMMInputScoreImputator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrVariantContextAnnotations.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LocationAndAlleles.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.MutectReadThreadingAssemblerArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMNativeArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupReadErrorCorrector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RefVsAnyResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.StandardPairHMMInputScoreImputator.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.mutect

├─ org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStats.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.SomaticRefVsAnyResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix.class - [JAR]

org.broadinstitute.hellbender.utils.functional

├─ org.broadinstitute.hellbender.utils.functional.IntBiConsumer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.functional.IntToDoubleBiFunction.class - [JAR]

org.broadinstitute.hellbender.utils.svd

├─ org.broadinstitute.hellbender.utils.svd.ApacheSingularValueDecomposer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.OjAlgoSingularValueDecomposer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.SVD.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.SVDFactory.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.SimpleSVD.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.svd.SparkSingularValueDecomposer.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.bqsr

├─ org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.genelistoutput

├─ org.broadinstitute.hellbender.tools.funcotator.genelistoutput.GeneListOutputRenderer.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.models

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionGlobalParameters.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionInitializer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionLikelihoods.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionModeller.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionPrior.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionSamplers.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionSegmentedData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionState.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioModeller.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioSamplers.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioSegmentedData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioState.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.FunctionCache.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.readorientation

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation.class - [JAR]

org.broadinstitute.hellbender

├─ org.broadinstitute.hellbender.CommandLineArgumentValidatorMain.class - [JAR]

├─ org.broadinstitute.hellbender.Main.class - [JAR]

org.broadinstitute.hellbender.exceptions

├─ org.broadinstitute.hellbender.exceptions.GATKException.class - [JAR]

├─ org.broadinstitute.hellbender.exceptions.PicardNonZeroExitException.class - [JAR]

├─ org.broadinstitute.hellbender.exceptions.UserException.class - [JAR]

org.broadinstitute.hellbender.utils.read.mergealignment

├─ org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.BestMapqPrimaryAlignmentSelectionStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.EarliestFragmentPrimaryAlignmentSelectionStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.MostDistantPrimaryAlignmentSelectionStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger.class - [JAR]

org.broadinstitute.hellbender.tools.spark.pathseq

├─ org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.MarkedOpticalDuplicateReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAligner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSTree.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils.optimization

├─ org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.qc

├─ org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.qc.Pileup.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.filters

├─ org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CompOverlap.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary.class - [JAR]

org.broadinstitute.hellbender.tools.spark.transforms

├─ org.broadinstitute.hellbender.tools.spark.transforms.ApplyBQSRSparkFn.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.transforms.BaseRecalibratorSparkFn.class - [JAR]

org.broadinstitute.hellbender.utils.variant.writers

├─ org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiningIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.HomRefBlock.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.writers.TLODBlock.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.genotyper

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleLikelihoodMatrixMapper.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.FRDBQDUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAlleleCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculators.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection.class - [JAR]

org.broadinstitute.hellbender.utils.variant

├─ org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.DbSnpVariantType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKVCFConstants.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKVariant.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.MinimalVariant.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.VariantContextGetters.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.variant.VcfUtils.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber

├─ org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.FilterIntervals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.ModelSegments.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals.class - [JAR]

org.broadinstitute.hellbender.metrics.analysis

├─ org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.rnaseq

├─ org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.class - [JAR]

org.broadinstitute.hellbender.tools

├─ org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags.class - [JAR]

├─ org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis.class - [JAR]

├─ org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.BwaMemIndexImageCreator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.ClipReads.class - [JAR]

├─ org.broadinstitute.hellbender.tools.CompareIntervalLists.class - [JAR]

├─ org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam.class - [JAR]

├─ org.broadinstitute.hellbender.tools.CountBases.class - [JAR]

├─ org.broadinstitute.hellbender.tools.CountReads.class - [JAR]

├─ org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard.class - [JAR]

├─ org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads.class - [JAR]

├─ org.broadinstitute.hellbender.tools.FlagStat.class - [JAR]

├─ org.broadinstitute.hellbender.tools.GatherVcfsCloud.class - [JAR]

├─ org.broadinstitute.hellbender.tools.GetSampleName.class - [JAR]

├─ org.broadinstitute.hellbender.tools.HaplotypeCallerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.HtsgetReader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.IndexFeatureFile.class - [JAR]

├─ org.broadinstitute.hellbender.tools.LeftAlignIndels.class - [JAR]

├─ org.broadinstitute.hellbender.tools.LocalAssembler.class - [JAR]

├─ org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.PrintDistantMates.class - [JAR]

├─ org.broadinstitute.hellbender.tools.PrintReads.class - [JAR]

├─ org.broadinstitute.hellbender.tools.PrintReadsHeader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.SplitReads.class - [JAR]

├─ org.broadinstitute.hellbender.tools.StructuralVariantDiscoverer.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable

├─ org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvLocatableTableCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.consensus

├─ org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI.class - [JAR]

org.broadinstitute.hellbender.utils.config

├─ org.broadinstitute.hellbender.utils.config.ConfigFactory.class - [JAR]

├─ org.broadinstitute.hellbender.utils.config.CustomBooleanConverter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.config.GATKConfig.class - [JAR]

├─ org.broadinstitute.hellbender.utils.config.SystemProperty.class - [JAR]

org.broadinstitute.hellbender.utils.iterators

├─ org.broadinstitute.hellbender.utils.iterators.AllLocusIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.ByteArrayIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.CloseAtEndIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.IntervalLocusIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.IntervalOverlappingIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.PushPullTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.PushToPullIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.ReadFilteringIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.ReadTransformingIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.SAMRecordToReadIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.iterators.ShardedIntervalIterator.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.realignmentfilter

├─ org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine.class - [JAR]

org.broadinstitute.hellbender.utils.report

├─ org.broadinstitute.hellbender.utils.report.GATKReport.class - [JAR]

├─ org.broadinstitute.hellbender.utils.report.GATKReportColumn.class - [JAR]

├─ org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat.class - [JAR]

├─ org.broadinstitute.hellbender.utils.report.GATKReportDataType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.report.GATKReportTable.class - [JAR]

├─ org.broadinstitute.hellbender.utils.report.GATKReportVersion.class - [JAR]

org.broadinstitute.hellbender.engine.spark

├─ org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.GATKRegistrator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.GATKSparkTool.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.LocusWalkerContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.NonChecksumLocalFileSystem.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.RangePartitionCoalescer.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.ReadWalkerContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SAMRecordSerializer.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SparkContextFactory.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.SparkSharder.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.VariantWalkerContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedAssembly.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContig.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContigGenerator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignmentInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigAlignmentsRDDProcessor.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AssemblyContigWithFineTunedAlignments.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.ContigAlignmentsModifier.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.StrandSwitch.class - [JAR]

org.broadinstitute.hellbender.tools.spark.bwa

├─ org.broadinstitute.hellbender.tools.spark.bwa.BwaArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.bwa.BwaSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.bwa.BwaSparkEngine.class - [JAR]

org.broadinstitute.hellbender.utils.fasta

├─ org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator

├─ org.broadinstitute.hellbender.tools.funcotator.AliasProvider.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.AminoAcid.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FlankSettings.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.Funcotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotationMap.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.Funcotator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorSegmentArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.OutputRenderer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.SequenceComparison.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode.class - [JAR]

org.broadinstitute.hellbender.utils.locusiterator

├─ org.broadinstitute.hellbender.utils.locusiterator.AlignmentContextIteratorBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.AlignmentStateMachine.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.IntervalAlignmentContextIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.LIBSDownsamplingInfo.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.LocusIteratorByState.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.PerSampleReadStateManager.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.ReadStateManager.class - [JAR]

├─ org.broadinstitute.hellbender.utils.locusiterator.SamplePartitioner.class - [JAR]

org.broadinstitute.hellbender.tools.spark.pipelines

├─ org.broadinstitute.hellbender.tools.spark.pipelines.BQSRPipelineSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.CountBasesSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.CountVariantsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.FlagStatSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.PrintReadsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.PrintVariantsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.ReadsPipelineSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pipelines.SortSamSpark.class - [JAR]

org.broadinstitute.hellbender.tools.sv

├─ org.broadinstitute.hellbender.tools.sv.BafEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.DepthEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.DiscordantPairEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.LocusDepth.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.PrintSVEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SVCallRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SVCallRecordWithEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SVLocatable.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SplitReadEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.sv.SplitReadSite.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.AdaptiveChainPruner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.CommonSuffixSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.LowWeightChainPruner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeCommonSuffices.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeDiamonds.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeTails.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedSequenceMerger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SplitCommonSuffices.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.VertexBasedTransformer.class - [JAR]

org.broadinstitute.hellbender.utils.read

├─ org.broadinstitute.hellbender.utils.read.AlignmentUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ArtificialReadIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ArtificialReadUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.BDGAlignmentRecordToGATKReadAdapter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.CigarBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.CigarUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.Fragment.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.GATKRead.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.GATKReadToBDGAlignmentRecordConverter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.GATKReadWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.HeaderlessSAMRecordCoordinateComparator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ReadConstants.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ReadUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.ReadsWriteFormat.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.mutect.filtering

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.AlleleFilterUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.sampileup

├─ org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupElement.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.mafOutput

├─ org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.LocatableFuncotationCreator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation.class - [JAR]

org.broadinstitute.hellbender.utils.gcs

├─ org.broadinstitute.hellbender.utils.gcs.BucketUtils.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.gcnv

├─ org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVIntervalVariantComposer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState.class - [JAR]

org.broadinstitute.hellbender.utils.dragstr

├─ org.broadinstitute.hellbender.utils.dragstr.DoubleSequence.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.DragstrParamUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.DragstrParams.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.DragstrParamsBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.DragstrReferenceAnalyzer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.STRTableFile.class - [JAR]

├─ org.broadinstitute.hellbender.utils.dragstr.STRTableFileBuilder.class - [JAR]

org.broadinstitute.hellbender.tools.walkers

├─ org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.CountVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.MethylationTypeCaller.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.PairWalker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.ReadAnonymizer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.RevertBaseQualityScores.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.SplitIntervals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.UnmarkDuplicates.class - [JAR]

org.broadinstitute.hellbender.tools.spark

├─ org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.CreateHadoopBamSplittingIndex.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.PileupSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.RevertSamSpark.class - [JAR]

org.broadinstitute.hellbender.utils.solver

├─ org.broadinstitute.hellbender.utils.solver.RobustBrentSolver.class - [JAR]

├─ org.broadinstitute.hellbender.utils.solver.SynchronizedUnivariateSolver.class - [JAR]

├─ org.broadinstitute.hellbender.utils.solver.UnivariateSolverJobDescription.class - [JAR]

├─ org.broadinstitute.hellbender.utils.solver.UnivariateSolverSpecifications.class - [JAR]

org.broadinstitute.hellbender.transformers

├─ org.broadinstitute.hellbender.transformers.AdapterTrimTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.BQSRReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.DUSTReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.IUPACReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.ReadTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.StripMateNumberTransformer.class - [JAR]

├─ org.broadinstitute.hellbender.transformers.VariantTransformer.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv

├─ org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistribution.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.InsertSizeDistributionShape.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.gtf

├─ org.broadinstitute.hellbender.utils.codecs.gtf.AbstractGtfCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.EnsemblGtfCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCDSFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfExonFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfFeatureBaseData.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfGeneFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfSelenocysteineFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStartCodonFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfStopCodonFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfTranscriptFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.gtf.GencodeGtfUTRFeature.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.vqsr

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.ApplyVQSR.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantTrain.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantWriteTensors.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.GatherTranches.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.GaussianMixtureModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.MultivariateGaussian.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.TensorType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.TrainingSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.Tranche.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.TrancheManager.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.TruthSensitivityTranche.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDatum.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine.class - [JAR]

org.broadinstitute.hellbender.tools.validation

├─ org.broadinstitute.hellbender.tools.validation.CompareBaseQualities.class - [JAR]

├─ org.broadinstitute.hellbender.tools.validation.CompareMatrix.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils.segmentation

├─ org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter.class - [JAR]

org.broadinstitute.hellbender.utils.runtime

├─ org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutputSnapshot.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.InputStreamSettings.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProcessController.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProcessOutput.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProcessSettings.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ProgressLogger.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.RuntimeUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.ScriptExecutorException.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.StreamLocation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.StreamOutput.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.class - [JAR]

├─ org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants.class - [JAR]

org.broadinstitute.hellbender.metrics

├─ org.broadinstitute.hellbender.metrics.InsertSizeMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MetricAccumulationLevel.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MetricsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MetricsUtils.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MultiLevelCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MultiLevelMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.PerUnitMetricCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.QualityYieldMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.SAMRecordAndReference.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.SAMRecordAndReferenceMultiLevelCollector.class - [JAR]

├─ org.broadinstitute.hellbender.metrics.SAMRecordMultiLevelCollector.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.caller

├─ org.broadinstitute.hellbender.tools.copynumber.caller.SimpleCopyRatioCaller.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv.utils

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.CNVInputReader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.ComplexityPartitioner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.ExternalCommandlineProgramModule.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.ExtractOriginalAlignmentRecordsByNameSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVReferenceUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFReader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.Strand.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.denoising

├─ org.broadinstitute.hellbender.tools.copynumber.denoising.GCBiasCorrector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals.class - [JAR]

org.broadinstitute.hellbender.tools.spark.validation

├─ org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark.class - [JAR]

org.broadinstitute.hellbender.tools.spark.pathseq.loggers

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterEmptyLogger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreLogger.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreMetrics.class - [JAR]

org.broadinstitute.hellbender.utils.mcmc

├─ org.broadinstitute.hellbender.utils.mcmc.AbstractSliceSampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.DataCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.Decile.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.DecileCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.GibbsSampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.Parameter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.ParameterEnum.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.ParameterSampler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.ParameterizedState.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.PosteriorSummary.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.PosteriorSummaryUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.mcmc.SliceSampler.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter.class - [JAR]

org.broadinstitute.hellbender.utils.activityprofile

├─ org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile.class - [JAR]

├─ org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileState.class - [JAR]

├─ org.broadinstitute.hellbender.utils.activityprofile.ActivityProfileStateRange.class - [JAR]

├─ org.broadinstitute.hellbender.utils.activityprofile.BandPassActivityProfile.class - [JAR]

org.broadinstitute.hellbender.tools.examples.metrics.single

├─ org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.varianteval

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalReportWriter.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.segmentation

├─ org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.segmentation.CopyRatioKernelSegmenter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.segmentation.MultisampleMultidimensionalKernelSegmenter.class - [JAR]

org.broadinstitute.hellbender.tools.spark.utils

├─ org.broadinstitute.hellbender.tools.spark.utils.FlatMapGluer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.HopscotchCollectionSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.HopscotchMapSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.HopscotchMultiMapSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.HopscotchSetSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.HopscotchUniqueMultiMapSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.IntHistogram.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.LargeLongHopscotchSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.LongBloomFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.LongHopscotchSet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.LongIterator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.ReadFilterSparkifier.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.utils.ReadTransformerSparkifier.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.copynumber

├─ org.broadinstitute.hellbender.utils.codecs.copynumber.SimpleCountCodec.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.contamination

├─ org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummaries.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.formats.records

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput

├─ org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput.SimpleTsvOutputRenderer.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils.genotyping

├─ org.broadinstitute.hellbender.tools.copynumber.utils.genotyping.NaiveHeterozygousPileupGenotypingUtils.class - [JAR]

org.broadinstitute.hellbender.utils.samples

├─ org.broadinstitute.hellbender.utils.samples.Affection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.MendelianViolation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.PedReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.PedigreeValidationType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.Sample.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.SampleDB.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.SampleDBBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.Sex.class - [JAR]

├─ org.broadinstitute.hellbender.utils.samples.Trio.class - [JAR]

org.broadinstitute.hellbender.utils.tsv

├─ org.broadinstitute.hellbender.utils.tsv.DataLine.class - [JAR]

├─ org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.tsv.TableColumnCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.tsv.TableReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.tsv.TableUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.tsv.TableWriter.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.arguments

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyHybridADVIArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticGenotypingArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection.class - [JAR]

org.broadinstitute.hellbender.cmdline.programgroups

├─ org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup.class - [JAR]

├─ org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.formats

├─ org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.sv

├─ org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.sv.SVCluster.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratNode.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratNodeIterator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.StratificationManager.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.Stratifier.class - [JAR]

org.broadinstitute.hellbender.utils

├─ org.broadinstitute.hellbender.utils.AutoCloseableReference.class - [JAR]

├─ org.broadinstitute.hellbender.utils.BaseUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.BinaryTableReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.BinaryTableWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.ByteMapIntervalPileup.class - [JAR]

├─ org.broadinstitute.hellbender.utils.ClassUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.CompressedDataList.class - [JAR]

├─ org.broadinstitute.hellbender.utils.DigammaCache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Dirichlet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.EmptyIntervalPileup.class - [JAR]

├─ org.broadinstitute.hellbender.utils.FisherExactTest.class - [JAR]

├─ org.broadinstitute.hellbender.utils.GenomeLoc.class - [JAR]

├─ org.broadinstitute.hellbender.utils.GenomeLocParser.class - [JAR]

├─ org.broadinstitute.hellbender.utils.GenomeLocSortedSet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.GenotypeCounts.class - [JAR]

├─ org.broadinstitute.hellbender.utils.GenotypeUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.HasGenomeLocation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Histogram.class - [JAR]

├─ org.broadinstitute.hellbender.utils.HttpUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IGVUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IndexRange.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IndexUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntegrationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntervalMergingRule.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntervalPileup.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntervalSetRule.class - [JAR]

├─ org.broadinstitute.hellbender.utils.IntervalUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.KV.class - [JAR]

├─ org.broadinstitute.hellbender.utils.LRUCache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Log10Cache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Log10FactorialCache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.LoggingUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.MRUCachingSAMSequenceDictionary.class - [JAR]

├─ org.broadinstitute.hellbender.utils.MannWhitneyU.class - [JAR]

├─ org.broadinstitute.hellbender.utils.MathUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.MatrixSummaryUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.NGSPlatform.class - [JAR]

├─ org.broadinstitute.hellbender.utils.NativeUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.NaturalLogUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Nucleotide.class - [JAR]

├─ org.broadinstitute.hellbender.utils.OptimizationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.QualityUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SATagBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SVInterval.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SVIntervalTree.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SequencerFlowClass.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SerializableFunction.class - [JAR]

├─ org.broadinstitute.hellbender.utils.SimpleInterval.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Tail.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Trilean.class - [JAR]

├─ org.broadinstitute.hellbender.utils.UniqueIDWrapper.class - [JAR]

├─ org.broadinstitute.hellbender.utils.UnsignedTypeUtil.class - [JAR]

├─ org.broadinstitute.hellbender.utils.Utils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.ZipUtils.class - [JAR]

org.broadinstitute.hellbender.utils.illumina

├─ org.broadinstitute.hellbender.utils.illumina.AdapterPair.class - [JAR]

├─ org.broadinstitute.hellbender.utils.illumina.IlluminaAdapterPair.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.fasta

├─ org.broadinstitute.hellbender.tools.walkers.fasta.CountBasesInReference.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils.class - [JAR]

org.broadinstitute.hellbender.utils.smithwaterman

├─ org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper.class - [JAR]

├─ org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner.class - [JAR]

├─ org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment.class - [JAR]

├─ org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants.class - [JAR]

├─ org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner.class - [JAR]

├─ org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner.class - [JAR]

org.broadinstitute.hellbender.utils.pileup

├─ org.broadinstitute.hellbender.utils.pileup.PileupElement.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pileup.ReadPileup.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.datacollection

├─ org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.formats.collections

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleLocatableCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleRecordCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AllelicCountCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.BaselineCopyNumberCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledCopyRatioSegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledLegacySegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyNumberPosteriorDistributionCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioSegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.CoveragePerContigCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.HDF5SimpleCountCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.IntegerCopyNumberSegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.LegacySegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.LinearCopyRatioCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.ModeledSegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.NonLocatableDoubleCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.OverlappingIntegerCopyNumberSegmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.ParameterDecileCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleIntervalCollection.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicSomaticShortMutationValidator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations.class - [JAR]

org.broadinstitute.hellbender.utils.nio

├─ org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults.class - [JAR]

├─ org.broadinstitute.hellbender.utils.nio.PathLineIterator.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.formats.metadata

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.MetadataUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata.class - [JAR]

org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation.class - [JAR]

org.broadinstitute.hellbender.utils.baq

├─ org.broadinstitute.hellbender.utils.baq.BAQ.class - [JAR]

org.broadinstitute.hellbender.utils.pairhmm

├─ org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.LoglessPairHMM.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.N2MemoryPairHMM.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.PairHMM.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel.class - [JAR]

├─ org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.class - [JAR]

org.broadinstitute.hellbender.utils.spark

├─ org.broadinstitute.hellbender.utils.spark.JoinReadsWithVariants.class - [JAR]

├─ org.broadinstitute.hellbender.utils.spark.SparkConverter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.spark.SparkUtils.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonOverlaps.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.vcfOutput

├─ org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleCount.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleFrequency.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CompFeatureInput.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Contig.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CpG.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Degeneracy.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.EvalFeatureInput.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Family.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Filter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FilterType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.FunctionalClass.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IndelSize.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.JexlExpression.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Novelty.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.SnpEffPositionModifier.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.TandemRepeat.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantType.class - [JAR]

org.broadinstitute.hellbender.utils.recalibration.covariates

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.varianteval.util

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.Analysis.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.AnalysisModuleScanner.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.DataPoint.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.EvaluationContext.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.SortableJexlVCMatchExp.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.varianteval.util.VariantEvalContext.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic

├─ org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging

├─ org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.SimpleGermlineTagger.class - [JAR]

org.broadinstitute.hellbender.utils.R

├─ org.broadinstitute.hellbender.utils.R.RScriptExecutor.class - [JAR]

├─ org.broadinstitute.hellbender.utils.R.RScriptExecutorException.class - [JAR]

├─ org.broadinstitute.hellbender.utils.R.RScriptLibrary.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.utils

├─ org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegions.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.mutect.clustering

├─ org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.variantutils

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.CalculateGenotypePosteriors.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.LeftAlignAndTrimVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.PosteriorProbabilitiesUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.ReblockGVCF.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable.class - [JAR]

org.broadinstitute.hellbender.utils.param

├─ org.broadinstitute.hellbender.utils.param.ParamUtils.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.filtrationRules

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyExacUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyGnomadUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHomvarFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ClinVarFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFiltrationRule.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.filtrationRules.TwoPassFuncotationFilter.class - [JAR]

org.broadinstitute.hellbender.utils.bwa

├─ org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache.class - [JAR]

org.broadinstitute.hellbender.tools.examples.metrics.multi

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector.class - [JAR]

├─ org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollectorArgs.class - [JAR]

org.broadinstitute.hellbender.utils.bigquery

├─ org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.bigquery.GATKAvroReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.bigquery.QueryRecord.class - [JAR]

├─ org.broadinstitute.hellbender.utils.bigquery.StorageAPIAvroReader.class - [JAR]

├─ org.broadinstitute.hellbender.utils.bigquery.TableReference.class - [JAR]

org.broadinstitute.hellbender.testutils

├─ org.broadinstitute.hellbender.testutils.TestingReadThreadingGraph.class - [JAR]

org.broadinstitute.hellbender.utils.fragments

├─ org.broadinstitute.hellbender.utils.fragments.FragmentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.fragments.FragmentUtils.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.annotator

├─ org.broadinstitute.hellbender.tools.walkers.annotator.AS_StrandBiasMutectAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.AlleleFraction.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.Annotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ClippingRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.CountNs.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.Coverage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.FeaturizedReadSets.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosRankSumTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.SampleList.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StandardHCAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.class - [JAR]

org.broadinstitute.hellbender.tools.spark.sv.discovery

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.AnnotatedVariantProducer.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.BreakEndVariantType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SVAlignmentLengthFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SVMappingQualityFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SimpleSVType.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.StructuralVariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoverFromLocalAssemblyContigAlignmentsSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputMetaData.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.sv.discovery.SvType.class - [JAR]

org.broadinstitute.hellbender.utils.recalibration

├─ org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.EventType.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.QualQuantizer.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.RecalDatum.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.RecalUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport.class - [JAR]

├─ org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables.class - [JAR]

org.broadinstitute.hellbender.utils.reference

├─ org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates.class - [JAR]

├─ org.broadinstitute.hellbender.utils.reference.ReferenceBases.class - [JAR]

├─ org.broadinstitute.hellbender.utils.reference.ReferenceUtils.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.metadata

├─ org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadata.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.metadata.FuncotationMetadataUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.metadata.SamplePairExtractor.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.metadata.TumorNormalPair.class - [JAR]

├─ org.broadinstitute.hellbender.tools.funcotator.metadata.VcfFuncotationMetadata.class - [JAR]

org.broadinstitute.hellbender.engine.spark.datasources

├─ org.broadinstitute.hellbender.engine.spark.datasources.DirectFullByteArrayByteAccess.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink.class - [JAR]

├─ org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource.class - [JAR]

org.broadinstitute.hellbender.engine.filters

├─ org.broadinstitute.hellbender.engine.filters.AlignmentAgreesWithHeaderReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.CountingReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.CountingVariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ExcessiveEndClippedReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.LibraryReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.MetricsReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.NotOpticalDuplicateReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.OverclippedReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.PlatformReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadGroupReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.ReadStrandFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.SampleReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.SoftClippedReadFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.VariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.VariantIDsVariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.filters.WellformedReadFilter.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator.class - [JAR]

org.broadinstitute.hellbender.utils.clipping

├─ org.broadinstitute.hellbender.utils.clipping.ClippingOp.class - [JAR]

├─ org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.clipping.ReadClipper.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper

├─ org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine.class - [JAR]

org.broadinstitute.hellbender.utils.help

├─ org.broadinstitute.hellbender.utils.help.GATKDocWorkUnit.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.GATKGSONWorkUnit.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.GATKHelpDocWorkUnitHandler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.GATKHelpDoclet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.GATKWDLDoclet.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.GATKWDLWorkUnitHandler.class - [JAR]

├─ org.broadinstitute.hellbender.utils.help.HelpConstants.class - [JAR]

org.broadinstitute.hellbender.tools.genomicsdb

├─ org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBArgumentCollection.class - [JAR]

├─ org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants.class - [JAR]

├─ org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.class - [JAR]

├─ org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBOptions.class - [JAR]

├─ org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBUtils.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.coverage

├─ org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.coverage.CoverageUtils.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType.class - [JAR]

org.broadinstitute.hellbender.utils.logging

├─ org.broadinstitute.hellbender.utils.logging.BunnyLog.class - [JAR]

├─ org.broadinstitute.hellbender.utils.logging.OneShotLogger.class - [JAR]

org.broadinstitute.hellbender.tools.htsgetreader

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetClass.class - [JAR]

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetErrorResponse.class - [JAR]

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetFormat.class - [JAR]

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestBuilder.class - [JAR]

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetRequestField.class - [JAR]

├─ org.broadinstitute.hellbender.tools.htsgetreader.HtsgetResponse.class - [JAR]

org.broadinstitute.hellbender.tools.walkers.validation

├─ org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.Concordance.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.ReferenceBlockConcordance.class - [JAR]

├─ org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.table

├─ org.broadinstitute.hellbender.utils.codecs.table.TableCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.table.TableFeature.class - [JAR]

org.broadinstitute.hellbender.engine

├─ org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ActivityProfileStateIterator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AlignmentContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AssemblyRegion.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AssemblyRegionIterator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.AssemblyRegionWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.BasicReference.class - [JAR]

├─ org.broadinstitute.hellbender.engine.DoNotSubclass.class - [JAR]

├─ org.broadinstitute.hellbender.engine.DuplicateSetWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureCache.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureInput.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureIntervalIterator.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureManager.class - [JAR]

├─ org.broadinstitute.hellbender.engine.FeatureWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.GATKDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.GATKPath.class - [JAR]

├─ org.broadinstitute.hellbender.engine.GATKTool.class - [JAR]

├─ org.broadinstitute.hellbender.engine.IntervalWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.LocusWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.LocusWalkerByInterval.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiIntervalShard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiVariantDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiVariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiplePassReadWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ProgressMeter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadContextData.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadsContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadsDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReadsPathDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceContext.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceDataSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceFileSource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceMemorySource.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceShard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ReferenceWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.Shard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ShardBoundary.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ShardBoundaryShard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter.class - [JAR]

├─ org.broadinstitute.hellbender.engine.TraversalParameters.class - [JAR]

├─ org.broadinstitute.hellbender.engine.TwoPassVariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.VariantLocusWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.VariantShard.class - [JAR]

├─ org.broadinstitute.hellbender.engine.VariantWalker.class - [JAR]

├─ org.broadinstitute.hellbender.engine.VariantWalkerBase.class - [JAR]

├─ org.broadinstitute.hellbender.engine.WalkerBase.class - [JAR]

org.broadinstitute.hellbender.utils.read.markduplicates

├─ org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy.class - [JAR]

├─ org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey.class - [JAR]

org.broadinstitute.hellbender.utils.codecs.refseq

├─ org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqCodec.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqFeature.class - [JAR]

├─ org.broadinstitute.hellbender.utils.codecs.refseq.RefSeqTranscript.class - [JAR]

org.broadinstitute.hellbender.tools.funcotator.compositeoutput

├─ org.broadinstitute.hellbender.tools.funcotator.compositeoutput.CompositeOutputRenderer.class - [JAR]

org.broadinstitute.hellbender.tools.copynumber.plotting

├─ org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments.class - [JAR]

├─ org.broadinstitute.hellbender.tools.copynumber.plotting.PlottingUtils.class - [JAR]

org.broadinstitute.hellbender.tools.readersplitters

├─ org.broadinstitute.hellbender.tools.readersplitters.LibraryNameSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.readersplitters.ReadGroupIdSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.readersplitters.ReadGroupSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter.class - [JAR]

├─ org.broadinstitute.hellbender.tools.readersplitters.SampleNameSplitter.class - [JAR]

org.broadinstitute.hellbender.tools.spark.transforms.markduplicates

├─ org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSpark.class - [JAR]

├─ org.broadinstitute.hellbender.tools.spark.transforms.markduplicates.MarkDuplicatesSparkUtils.class - [JAR]

org.broadinstitute.hellbender.utils.text

├─ org.broadinstitute.hellbender.utils.text.TextFormattingUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.text.XReadLines.class - [JAR]

htsjdk.samtools

├─ htsjdk.samtools.SAMRecordSparkCodec.class - [JAR]

org.broadinstitute.hellbender.utils.io

├─ org.broadinstitute.hellbender.utils.io.BlockCompressedIntervalStream.class - [JAR]

├─ org.broadinstitute.hellbender.utils.io.DeleteRecursivelyOnExitPathHook.class - [JAR]

├─ org.broadinstitute.hellbender.utils.io.FeatureOutputStream.class - [JAR]

├─ org.broadinstitute.hellbender.utils.io.HardThresholdingOutputStream.class - [JAR]

├─ org.broadinstitute.hellbender.utils.io.IOUtils.class - [JAR]

├─ org.broadinstitute.hellbender.utils.io.Resource.class - [JAR]

org.broadinstitute.hellbender.utils.haplotype

├─ org.broadinstitute.hellbender.utils.haplotype.EventMap.class - [JAR]

├─ org.broadinstitute.hellbender.utils.haplotype.Haplotype.class - [JAR]

├─ org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination.class - [JAR]

├─ org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.class - [JAR]

├─ org.broadinstitute.hellbender.utils.haplotype.SAMFileDestination.class - [JAR]

org.broadinstitute.hellbender.utils.genotyper

├─ org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.AlleleList.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.AlleleListPermutation.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.GenotypePriorCalculator.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.IndexedAlleleList.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.IndexedSampleList.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.LikelihoodMatrix.class - [JAR]

├─ org.broadinstitute.hellbender.utils.genotyper.SampleList.class - [JAR]

org.broadinstitute : gatk

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