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    Download gatk JAR 4.6.1.0 with all dependencies


    Development on GATK 4

    Files of the artifact gatk version 4.6.1.0 from the group org.broadinstitute.

    Test

    Download gatk (4.6.1.0)
    Artifact gatk
    Group org.broadinstitute
    Version 4.6.1.0
    Last update 24. October 2024
    Organization not specified
    URL http://github.com/broadinstitute/gatk
    License BSD 3-Clause
    Dependencies amount 45
    Dependencies barclay, owner, picard, genomicsdb, opencsv, guava, htsjdk, google-cloud-nio-GATK4-custom-patch, gov.nist.math.jama, gcs-connector, log4j-api, log4j-core, commons-lang3, commons-math3, commons-collections4, commons-vfs2, commons-io, reflections, fastutil, JTransforms, hdf5-java-bindings, gatk-native-bindings, ojalgo, ojalgo-commons-math3, spark-mllib_2.11, bdg-formats, adam-core-spark2_2.11, jgrapht-core, testng, hadoop-minicluster, hadoop-bam, hadoop-client, jsr203hadoop, kryo-serializers, netlib-native_ref-osx-x86_64, netlib-native_ref-linux-x86_64, netlib-native_system-linux-x86_64, netlib-native_system-osx-x86_64, kryo, reflectasm, gkl, gatk-bwamem-jni, gatk-fermilite-jni, sqlite-jdbc, objenesis,
    There are maybe transitive dependencies!
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    3 downloads

    Source code of gatk version 4.6.1.0

    META-INF
    META-INF.META-INF.MANIFEST.MF
    htsjdk.samtools
    htsjdk.samtools.htsjdk.samtools.SAMRecordSparkCodec
    large.nvscorevariants
    large.nvscorevariants.large.nvscorevariants.1d_cnn_mix_train_full_bn.pt
    large.nvscorevariants.large.nvscorevariants.small_2d.pt
    large
    large.large.testResourceFile.txt
    .log4j.properties
    .log4j2.xml
    org.broadinstitute.hellbender
    org.broadinstitute.hellbender.org.broadinstitute.hellbender.CommandLineArgumentValidatorMain
    org.broadinstitute.hellbender.org.broadinstitute.hellbender.Main
    org.broadinstitute.hellbender.cmdline
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.CommandLineArgumentValidator
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.CommandLineProgram
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.DeprecatedToolsRegistry
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions
    org.broadinstitute.hellbender.cmdline.GATKPlugin
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKReadFilterArgumentCollection
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationArgumentCollection
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterArgumentCollection
    org.broadinstitute.hellbender.cmdline.GATKPlugin.org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor
    org.broadinstitute.hellbender.cmdline
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.ModeArgumentUtils
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.ReadFilterArgumentDefinitions
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions
    org.broadinstitute.hellbender.cmdline.org.broadinstitute.hellbender.cmdline.TestProgramGroup
    org.broadinstitute.hellbender.cmdline.argumentcollections
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.MarkDuplicatesSparkArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.MetricAccumulationLevelArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.MultiVariantInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OpticalDuplicatesArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalFeatureInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalIntervalArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReadInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalReferenceInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalTextOutputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.OptionalVariantInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.ReadInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.ReferenceInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredFeatureInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredIntervalArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReadInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredReferenceInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.RequiredVariantInputArgumentCollection
    org.broadinstitute.hellbender.cmdline.argumentcollections.org.broadinstitute.hellbender.cmdline.argumentcollections.SequenceDictionaryValidationArgumentCollection
    org.broadinstitute.hellbender.cmdline.programgroups
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.CoverageAnalysisProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.FlowBasedProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.MetagenomicsProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.MethylationProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup
    org.broadinstitute.hellbender.cmdline.programgroups.org.broadinstitute.hellbender.cmdline.programgroups.StructuralVariantDiscoveryProgramGroup
    org.broadinstitute.hellbender.engine
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ActivityProfileStateIterator
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AlignmentAndReferenceContext
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AlignmentContext
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AssemblyRegion
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AssemblyRegionIterator
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.AssemblyRegionWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.BasicReference
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.DoNotSubclass
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.DuplicateSetWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureCache
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureContext
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureInput
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureIntervalIterator
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureManager
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.FeatureWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.GATKDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.GATKPath
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.GATKTool
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.IntervalWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.LocusWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.LocusWalkerByInterval
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiFeatureWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiIntervalShard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiVariantDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiVariantWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedByOverlap
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiplePassReadWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.PartialReadWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ProgressMeter
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadContextData
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadsContext
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadsDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReadsPathDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceContext
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceDataSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceFileSource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceMemorySource
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceShard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ReferenceWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.Shard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ShardBoundary
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ShardBoundaryShard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.TraversalParameters
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.TwoPassVariantWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.VariantLocusWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.VariantShard
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.VariantWalker
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.VariantWalkerBase
    org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.WalkerBase
    org.broadinstitute.hellbender.engine.filters
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.AlignmentAgreesWithHeaderReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.AmbiguousBaseReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.CountingReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.CountingVariantFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ExcessiveEndClippedReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.FragmentLengthReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.JexlExpressionReadTagValueFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.LibraryReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.MappingQualityReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.MateDistantReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.MetricsReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.NotOpticalDuplicateReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.OverclippedReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.PlatformReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.PlatformUnitReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadGroupBlackListReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadGroupReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadLengthReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadNameReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadStrandFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.ReadTagValueFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.SampleReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.SoftClippedReadFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.VariantFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.VariantFilterLibrary
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.VariantIDsVariantFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.VariantTypesVariantFilter
    org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.WellformedReadFilter
    org.broadinstitute.hellbender.engine.filters.flow
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.FlowBasedHmerBasedReadFilterHelper
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeSymetricReadFilter
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.FlowBasedTPAttributeValidReadFilter
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.HmerQualitySymetricReadFilter
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.ReadGroupHasFlowOrderReadFilter
    org.broadinstitute.hellbender.engine.filters.flow.org.broadinstitute.hellbender.engine.filters.flow.WellformedFlowBasedReadFilter
    org.broadinstitute.hellbender.engine.spark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AddContextDataToReadSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AddContextDataToReadSparkOptimized
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AssemblyRegionArgumentCollection
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AssemblyRegionReadShardArgumentCollection
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerContext
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.AssemblyRegionWalkerSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.FindAssemblyRegionsSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.GATKRegistrator
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.GATKSparkTool
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.IntervalWalkerContext
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.IntervalWalkerSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.LocusWalkerContext
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.NonChecksumLocalFileSystem
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.RangePartitionCoalescer
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.ReadWalkerContext
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SAMRecordSerializer
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SAMRecordToGATKReadAdapterSerializer
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SparkCommandLineArgumentCollection
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SparkContextFactory
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.SparkSharder
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.VariantWalkerContext
    org.broadinstitute.hellbender.engine.spark.org.broadinstitute.hellbender.engine.spark.VariantWalkerSpark
    org.broadinstitute.hellbender.engine.spark.datasources
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceFileSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceHadoopSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceMultiSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSparkSource
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.ReferenceWindowFunctions
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSink
    org.broadinstitute.hellbender.engine.spark.datasources.org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource
    org.broadinstitute.hellbender.exceptions
    org.broadinstitute.hellbender.exceptions.org.broadinstitute.hellbender.exceptions.GATKException
    org.broadinstitute.hellbender.exceptions.org.broadinstitute.hellbender.exceptions.PicardNonZeroExitException
    org.broadinstitute.hellbender.exceptions.org.broadinstitute.hellbender.exceptions.UserException
    org.broadinstitute.hellbender.metrics
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.InsertSizeMetrics
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.InsertSizeMetricsArgumentCollection
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MetricAccumulationLevel
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MetricsArgumentCollection
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MetricsUtils
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MultiLevelCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MultiLevelMetrics
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.PerUnitMetricCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.QualityYieldMetrics
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.QualityYieldMetricsArgumentCollection
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.SAMRecordAndReference
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.SAMRecordAndReferenceMultiLevelCollector
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.SAMRecordMultiLevelCollector
    org.broadinstitute.hellbender.metrics.analysis
    org.broadinstitute.hellbender.metrics.analysis.org.broadinstitute.hellbender.metrics.analysis.AlleleFrequencyQCMetric
    org.broadinstitute.hellbender.metrics.analysis.org.broadinstitute.hellbender.metrics.analysis.BaseDistributionByCycleMetrics
    org.broadinstitute.hellbender.metrics
    org.broadinstitute.hellbender.metrics.org.broadinstitute.hellbender.metrics.insertSizeHistogram.R
    org.broadinstitute.hellbender.testutils
    org.broadinstitute.hellbender.testutils.org.broadinstitute.hellbender.testutils.TestingReadThreadingGraph
    org.broadinstitute.hellbender.tools
    org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.AddOriginalAlignmentTags
    org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.AnalyzeSaturationMutagenesis
    org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection
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    org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
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    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts
    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
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    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.ModelSegments
    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
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    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection
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    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyHybridADVIArgumentCollection
    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineContigPloidyModelArgumentCollection
    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection
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    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticModelingArgumentCollection
    org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.SomaticSegmentationArgumentCollection
    org.broadinstitute.hellbender.tools.copynumber.caller
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    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.case_determine_ploidy_and_depth.py
    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.cohort_denoising_calling.py
    org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.cohort_determine_ploidy_and_depth.py
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    org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
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    org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
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    org.broadinstitute.hellbender.tools.copynumber.segmentation.org.broadinstitute.hellbender.tools.copynumber.segmentation.MultisampleMultidimensionalKernelSegmenter
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    org.broadinstitute.hellbender.tools.dragstr.org.broadinstitute.hellbender.tools.dragstr.StratifiedDragstrLocusCases
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    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalkerSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleFeatureWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleIntervalWalkerSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleLocusWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleLocusWalkerSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleMultiFeatureWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExamplePartialReadWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExamplePostTraversalPythonExecutor
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariants
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithVariantsSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleReferenceWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleStreamingPythonExecutor
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleTwoPassVariantWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleVariantWalker
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleVariantWalkerSpark
    org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.copyInputFileToOutputFile.py
    org.broadinstitute.hellbender.tools.examples.metrics.multi
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleCollectMultiMetricsSpark
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetrics
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsArgumentCollection
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollector
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.ExampleMultiMetricsCollectorSpark
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollector
    org.broadinstitute.hellbender.tools.examples.metrics.multi.org.broadinstitute.hellbender.tools.examples.metrics.multi.PerUnitExampleMultiMetricsCollectorArgs
    org.broadinstitute.hellbender.tools.examples.metrics.single
    org.broadinstitute.hellbender.tools.examples.metrics.single.org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleCollectSingleMetricsSpark
    org.broadinstitute.hellbender.tools.examples.metrics.single.org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetrics
    org.broadinstitute.hellbender.tools.examples.metrics.single.org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsArgumentCollection
    org.broadinstitute.hellbender.tools.examples.metrics.single.org.broadinstitute.hellbender.tools.examples.metrics.single.ExampleSingleMetricsCollectorSpark
    org.broadinstitute.hellbender.tools.filediagnostics
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.BAIAnalyzer
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.CRAIAnalyzer
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.CRAMAnalyzer
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.CRAMIssue8768Analyzer
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.HTSAnalyzer
    org.broadinstitute.hellbender.tools.filediagnostics.org.broadinstitute.hellbender.tools.filediagnostics.HTSAnalyzerFactory
    org.broadinstitute.hellbender.tools.funcotator
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.AliasProvider
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.AminoAcid
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.AnnotatedIntervalToSegmentVariantContextConverter
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.BaseFuncotatorArgumentCollection
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsConstants
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FilterFuncotationsUtils
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FlankSettings
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotateSegments
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.Funcotation
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotationMap
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.Funcotator
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorArgumentDefinitions
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorConstants
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorSegmentArgumentCollection
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.FuncotatorVariantArgumentCollection
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.Homo_sapiens_assembly19.dict
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.OutputRenderer
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.ProteinChangeInfo
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.SequenceComparison
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedAllele
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.StrandCorrectedReferenceBases
    org.broadinstitute.hellbender.tools.funcotator.org.broadinstitute.hellbender.tools.funcotator.TranscriptSelectionMode
    org.broadinstitute.hellbender.tools.funcotator.compositeoutput
    org.broadinstitute.hellbender.tools.funcotator.compositeoutput.org.broadinstitute.hellbender.tools.funcotator.compositeoutput.CompositeOutputRenderer
    org.broadinstitute.hellbender.tools.funcotator.dataSources
    org.broadinstitute.hellbender.tools.funcotator.dataSources.org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils
    org.broadinstitute.hellbender.tools.funcotator.dataSources.org.broadinstitute.hellbender.tools.funcotator.dataSources.LocatableFuncotationCreator
    org.broadinstitute.hellbender.tools.funcotator.dataSources.org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation
    org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
    org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic.CosmicFuncotationFactory
    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation
    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationBuilder
    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory
    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
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    org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment.SegmentExonUtils
    org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
    org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf.VcfFuncotationFactory
    org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
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    org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv.SimpleKeyXsvFuncotationFactory
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules
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    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyGnomadUtils
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AlleleFrequencyUtils
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHomvarFilter
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.AutosomalRecessiveConstants
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    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.FuncotationFiltrationRule
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LmmFilter
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.LofFilter
    org.broadinstitute.hellbender.tools.funcotator.filtrationRules.org.broadinstitute.hellbender.tools.funcotator.filtrationRules.TwoPassFuncotationFilter
    org.broadinstitute.hellbender.tools.funcotator
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    org.broadinstitute.hellbender.tools.funcotator.mafOutput
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    org.broadinstitute.hellbender.tools.funcotator.mafOutput.org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRenderer
    org.broadinstitute.hellbender.tools.funcotator.mafOutput.org.broadinstitute.hellbender.tools.funcotator.mafOutput.MafOutputRendererConstants
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    org.broadinstitute.hellbender.tools.readersplitters
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    org.broadinstitute.hellbender.tools.readersplitters.org.broadinstitute.hellbender.tools.readersplitters.ReaderSplitter
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    org.broadinstitute.hellbender.tools.reference
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    org.broadinstitute.hellbender.tools.reference.org.broadinstitute.hellbender.tools.reference.ReferencePair
    org.broadinstitute.hellbender.tools.reference.org.broadinstitute.hellbender.tools.reference.ReferenceSequenceTable
    org.broadinstitute.hellbender.tools.spark
    org.broadinstitute.hellbender.tools.spark.org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark
    org.broadinstitute.hellbender.tools.spark.org.broadinstitute.hellbender.tools.spark.BaseRecalibratorSpark
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    org.broadinstitute.hellbender.tools.spark.org.broadinstitute.hellbender.tools.spark.ParallelCopyGCSDirectoryIntoHDFSSpark
    org.broadinstitute.hellbender.tools.spark.org.broadinstitute.hellbender.tools.spark.PileupSpark
    org.broadinstitute.hellbender.tools.spark.org.broadinstitute.hellbender.tools.spark.RevertSamSpark
    org.broadinstitute.hellbender.tools.spark.bwa
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    org.broadinstitute.hellbender.tools.spark.pathseq.org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
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    org.broadinstitute.hellbender.tools.spark.pathseq.org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
    org.broadinstitute.hellbender.tools.spark.pathseq.org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
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    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterFileLogger
    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterLogger
    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSFilterMetrics
    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreFileLogger
    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreLogger
    org.broadinstitute.hellbender.tools.spark.pathseq.loggers.org.broadinstitute.hellbender.tools.spark.pathseq.loggers.PSScoreMetrics
    org.broadinstitute.hellbender.tools.spark.pipelines
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    org.broadinstitute.hellbender.tools.spark.pipelines.org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark
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    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.AllelePseudoDepth
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.Annotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.AnnotationUtils
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.AssemblyComplexity
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.BaseQuality
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityHistogram
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.BaseQualityRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.ChromosomeCounts
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.ClippingRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.CountNs
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.Coverage
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerAlleleBySample
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.DepthPerSampleHC
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.ExcessHet
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.FisherStrand
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.FragmentDepthPerAlleleBySample
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.FragmentLength
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.GenotypeSummaries
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.HaplotypeFilteringAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.HeterozygosityCalculator
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.InbreedingCoeff
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.JumboGenotypeAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.JumboInfoAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.LikelihoodRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.MappingQuality
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.MappingQualityZero
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.OrientationBiasReadCounts
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.OriginalAlignment
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.PedigreeAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.PerAlleleAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.QualByDepth
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.RankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.RawGtCount
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    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.ReadPosition
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.SampleList
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    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.StandardHCAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasBySample
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.StrandBiasTest
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.StrandOddsRatio
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.TransmittedSingleton
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.UniqueAltReadCount
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine
    org.broadinstitute.hellbender.tools.walkers.annotator.org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_BaseQualityRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_FisherStrand
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_InbreedingCoeff
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_MappingQualityRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_QualByDepth
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RMSMappingQuality
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_RankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_ReadPosRankSumTest
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StandardAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandBiasTest
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AS_StrandOddsRatio
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.AlleleSpecificAnnotationData
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData
    org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.StrandBiasUtils
    org.broadinstitute.hellbender.tools.walkers.annotator.flow
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    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.FlowAnnotatorBase
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.GcContent
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelLength
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerIndelNuc
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.HmerMotifs
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelClassify
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.IndelLength
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.StandardFlowBasedAnnotation
    org.broadinstitute.hellbender.tools.walkers.annotator.flow.org.broadinstitute.hellbender.tools.walkers.annotator.flow.VariantType
    org.broadinstitute.hellbender.tools.walkers.bqsr
    org.broadinstitute.hellbender.tools.walkers.bqsr.org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates
    org.broadinstitute.hellbender.tools.walkers.bqsr.org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR
    org.broadinstitute.hellbender.tools.walkers.bqsr.org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator
    org.broadinstitute.hellbender.tools.walkers.bqsr.org.broadinstitute.hellbender.tools.walkers.bqsr.GatherBQSRReports
    org.broadinstitute.hellbender.tools.walkers.consensus
    org.broadinstitute.hellbender.tools.walkers.consensus.org.broadinstitute.hellbender.tools.walkers.consensus.DownsampleByDuplicateSet
    org.broadinstitute.hellbender.tools.walkers.consensus.org.broadinstitute.hellbender.tools.walkers.consensus.MoleculeID
    org.broadinstitute.hellbender.tools.walkers.consensus.org.broadinstitute.hellbender.tools.walkers.consensus.ReadsWithSameUMI
    org.broadinstitute.hellbender.tools.walkers.contamination
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationModel
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationSegmenter
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.GatherPileupSummaries
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.MinorAlleleFractionRecord
    org.broadinstitute.hellbender.tools.walkers.contamination.org.broadinstitute.hellbender.tools.walkers.contamination.PileupSummary
    org.broadinstitute.hellbender.tools.walkers.conversion
    org.broadinstitute.hellbender.tools.walkers.conversion.org.broadinstitute.hellbender.tools.walkers.conversion.GtfInfo
    org.broadinstitute.hellbender.tools.walkers.conversion.org.broadinstitute.hellbender.tools.walkers.conversion.GtfToBed
    org.broadinstitute.hellbender.tools.walkers.coverage
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.CoverageOutputWriter
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.CoverageUtils
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverage
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoveragePartitionedDataStore
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.DepthOfCoverageStats
    org.broadinstitute.hellbender.tools.walkers.coverage.org.broadinstitute.hellbender.tools.walkers.coverage.DoCOutputType
    org.broadinstitute.hellbender.tools.walkers.fasta
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    org.broadinstitute.hellbender.tools.walkers.fasta.org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker
    org.broadinstitute.hellbender.tools.walkers.fasta.org.broadinstitute.hellbender.tools.walkers.fasta.FastaReferenceMaker
    org.broadinstitute.hellbender.tools.walkers.fasta.org.broadinstitute.hellbender.tools.walkers.fasta.ShiftFasta
    org.broadinstitute.hellbender.tools.walkers.featuremapping
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQuality
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.AddFlowSNVQualityArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.FeatureMapper
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapper
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowFeatureMapperArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.FlowPairHMMAlignReadsToHaplotypes
    org.broadinstitute.hellbender.tools.walkers.featuremapping.org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper
    org.broadinstitute.hellbender.tools.walkers.filters
    org.broadinstitute.hellbender.tools.walkers.filters.org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration
    org.broadinstitute.hellbender.tools.walkers.genotyper
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    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.AlleleSubsettingUtils
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.DRAGENGenotypesModel
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.FRDBQDUtils
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    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeAssignmentMethod
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeCalculationArgumentCollection
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    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculator
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodCalculatorDRAGEN
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypesCache
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    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingLikelihoods
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingModel
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.HeterogeneousPloidyModel
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.HomogeneousPloidyModel
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.IndependentSampleGenotypesModel
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine
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    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.StandardCallerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.UnifiedArgumentCollection
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    org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
    org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
    org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyper
    org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper.GnarlyGenotyperEngine
    org.broadinstitute.hellbender.tools.walkers.groundtruth
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.AddFlowBaseQuality
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.AncestralContigLocationTranslator
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthReadsBuilder
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.GroundTruthScorer
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.LocationTranslationException
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.SeriesStats
    org.broadinstitute.hellbender.tools.walkers.groundtruth.org.broadinstitute.hellbender.tools.walkers.groundtruth.SingleFileLocationTranslator
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller
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    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFilteringHC
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleFilteringMutect
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AlleleLikelihoodWriter
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResult
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyResultSet
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.CalledHaplotypes
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ConciseAlleleLikelihoodWriter
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrPairHMMInputScoreImputator
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.DragstrVariantContextAnnotations
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedAlignmentLikelihoodEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.FlowBasedHMMEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingDebugger
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerReadThreadingAssemblerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.KMerCounter
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.Kmer
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LikelihoodEngineArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.LongHomopolymerHaplotypeCollapsingEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.MutectReadThreadingAssemblerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NearbyKmerErrorCorrector
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.NonSymmetricalPairHMMInputScoreImputator
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.OccurrenceMatrix
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PDPairHMMLikelihoodCalculationEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMNativeArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PartiallyDeterminedHaplotypeComputationEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupDetectionArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PileupReadErrorCorrector
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCaller
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RampedHaplotypeCallerEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadErrorCorrector
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadLikelihoodCalculationEngine
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReadThreadingAssemblerArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.RefVsAnyResult
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceMode
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceResult
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceUtils
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.StandardPairHMMInputScoreImputator
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.AdaptiveChainPruner
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseEdge
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseGraph
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.BaseVertex
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.ChainPruner
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.CommonSuffixSplitter
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphBasedKBestHaplotypeFinder
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.GraphUtils
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.InverseAllele
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JTBestHaplotype
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.JunctionTreeKBestHaplotypeFinder
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotype
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KBestHaplotypeFinder
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.KmerSearchableGraph
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.LowWeightChainPruner
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeCommonSuffices
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeDiamonds
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MergeTails
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.MultiSampleEdge
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.Path
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqGraph
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SeqVertex
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedSequenceMerger
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SharedVertexSequenceSplitter
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.SplitCommonSuffices
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs.VertexBasedTransformer
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.AssemblerOffRamp
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OffRampBase
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.OnRampBase
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostAssemblerOnRamp
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PostFilterOnRamp
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.PreFilterOffRamp
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampBase
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps.RampUtils
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.AbstractReadThreadingGraph
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.JunctionTreeLinkedDeBruijnGraph
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.MultiDeBruijnVertex
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler
    org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
    org.broadinstitute.hellbender.tools.walkers.mutect
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.FeaturizedReadSets
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.GatherNormalArtifactData
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.GetNormalArtifactData
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStats
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.Mutect3DatasetEngine
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.MutectStats
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.NormalArtifactRecord
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.PerAlleleCollection
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.SomaticLikelihoodsEngine
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.SomaticRefVsAnyResult
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.SomaticReferenceConfidenceModel
    org.broadinstitute.hellbender.tools.walkers.mutect.org.broadinstitute.hellbender.tools.walkers.mutect.SubsettedLikelihoodMatrix
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.AlleleFractionCluster
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BetaBinomialCluster
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.BinomialCluster
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.Datum
    org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering
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    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.BaseQualityFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ClusteredEventsFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.DuplicatedAltReadFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorType
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterStats
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteringOutputStats
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FragmentLengthFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.GermlineFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardAlleleFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.HardFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.M2FiltersArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MTLowHeteroplasmyFilterTool
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MappingQualityFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MinAlleleFractionFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.MultiallelicFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2AlleleFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2Filter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NRatioFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NormalArtifactFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.NuMTFilterTool
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PanelOfNormalsFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.PolymeraseSlippageFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadOrientationFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ReadPositionFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrandArtifactFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.StrictStrandBiasFilter
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ThresholdCalculator
    org.broadinstitute.hellbender.tools.walkers.mutect.filtering.org.broadinstitute.hellbender.tools.walkers.mutect.filtering.TumorEvidenceFilter
    org.broadinstitute.hellbender.tools.walkers.qc
    org.broadinstitute.hellbender.tools.walkers.qc.org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup
    org.broadinstitute.hellbender.tools.walkers.qc.org.broadinstitute.hellbender.tools.walkers.qc.Pileup
    org.broadinstitute.hellbender.tools.walkers.qc.org.broadinstitute.hellbender.tools.walkers.qc.PostProcessReadsForRSEM
    org.broadinstitute.hellbender.tools.walkers.qc.org.broadinstitute.hellbender.tools.walkers.qc.ReadPair
    org.broadinstitute.hellbender.tools.walkers.qc.org.broadinstitute.hellbender.tools.walkers.qc.TransferReadTags
    org.broadinstitute.hellbender.tools.walkers.readorientation
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.AltSiteRecord
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPrior
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactPriorCollection
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.ArtifactState
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.BetaDistributionShape
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2Counts
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.CollectF1R2CountsArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.DepthOneHistograms
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2CountsCollector
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterConstants
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.F1R2FilterUtils
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModel
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine
    org.broadinstitute.hellbender.tools.walkers.readorientation.org.broadinstitute.hellbender.tools.walkers.readorientation.ReadOrientation
    org.broadinstitute.hellbender.tools.walkers.realignmentfilter
    org.broadinstitute.hellbender.tools.walkers.realignmentfilter.org.broadinstitute.hellbender.tools.walkers.realignmentfilter.FilterAlignmentArtifacts
    org.broadinstitute.hellbender.tools.walkers.realignmentfilter.org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.realignmentfilter.org.broadinstitute.hellbender.tools.walkers.realignmentfilter.RealignmentEngine
    org.broadinstitute.hellbender.tools.walkers.rnaseq
    org.broadinstitute.hellbender.tools.walkers.rnaseq.org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter
    org.broadinstitute.hellbender.tools.walkers.rnaseq.org.broadinstitute.hellbender.tools.walkers.rnaseq.GeneExpressionEvaluation
    org.broadinstitute.hellbender.tools.walkers.rnaseq.org.broadinstitute.hellbender.tools.walkers.rnaseq.OverhangFixingManager
    org.broadinstitute.hellbender.tools.walkers.rnaseq.org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
    org.broadinstitute.hellbender.tools.walkers.sv
    org.broadinstitute.hellbender.tools.walkers.sv.org.broadinstitute.hellbender.tools.walkers.sv.CollectSVEvidence
    org.broadinstitute.hellbender.tools.walkers.sv.org.broadinstitute.hellbender.tools.walkers.sv.JointGermlineCNVSegmentation
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    org.broadinstitute.hellbender.tools.walkers.validation
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    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithExpectedAlleleFraction
    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.CalculateMixingFractions
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    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.EvaluateInfoFieldConcordance
    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.FalsePositiveRecord
    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.FilterAnalysisRecord
    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.InfoConcordanceRecord
    org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.MergeMutect2CallsWithMC3
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    org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
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    org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BasicValidationResult
    org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.BetaBinomialDistribution
    org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.PowerCalculationUtils
    org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.ValidateBasicSomaticShortMutations
    org.broadinstitute.hellbender.tools.walkers.varianteval
    org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.AlleleFrequencyQC
    org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval
    org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalEngine
    org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalReportWriter
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
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    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.CountVariants
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.GenotypeFilterSummary
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelLengthHistogram
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.IndelSummary
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MendelianViolationEvaluator
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MetricsCollection
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.MultiallelicSummary
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.PrintMissingComp
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.StandardEval
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ThetaVariantEvaluator
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.TiTvVariantEvaluator
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.ValidationReport
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantAFEvaluator
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantEvaluator
    org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators.VariantSummary
    org.broadinstitute.hellbender.tools.walkers.varianteval
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    org.broadinstitute.hellbender.tools.walkers.variantutils
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    org.broadinstitute.hellbender.tools.walkers.vqsr
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    org.broadinstitute.hellbender.tools.walkers.vqsr.org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorArgumentCollection
    org.broadinstitute.hellbender.tools.walkers.vqsr.org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibratorEngine
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    org.broadinstitute.hellbender.tools.walkers.vqsr.org.broadinstitute.hellbender.tools.walkers.vqsr.plot_Tranches.R
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
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    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.LabeledVariantAnnotationsWalker
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.ScoreVariantAnnotations
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.TrainVariantAnnotationsModel
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.LabeledVariantAnnotationsData
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    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data.VariantType
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
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    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.isolation-forest.py
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
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    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonVariantAnnotationsModel
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.PythonVariantAnnotationsScorer
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    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsModelBackend
    org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling.VariantAnnotationsScorer
    org.broadinstitute.hellbender.transformers
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.AdapterTrimTransformer
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.BQSRReadTransformer
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    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.DRAGENMappingQualityReadTransformer
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.DUSTReadTransformer
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.IUPACReadTransformer
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer
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    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer
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    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.StripMateNumberTransformer
    org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.VariantTransformer
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    org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenomeLocSortedSet
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    org.broadinstitute.hellbender.utils.logging.org.broadinstitute.hellbender.utils.logging.BunnyLog
    org.broadinstitute.hellbender.utils.logging.org.broadinstitute.hellbender.utils.logging.OneShotLogger
    org.broadinstitute.hellbender.utils.mcmc
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.AbstractSliceSampler
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.AdaptiveMetropolisSampler
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.DataCollection
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.Decile
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.DecileCollection
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.GibbsSampler
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.MinibatchSliceSampler
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.Parameter
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.ParameterEnum
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.ParameterSampler
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.ParameterTableColumn
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.ParameterizedModel
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.ParameterizedState
    org.broadinstitute.hellbender.utils.mcmc.org.broadinstitute.hellbender.utils.mcmc.SliceSampler
    org.broadinstitute.hellbender.utils.nio
    org.broadinstitute.hellbender.utils.nio.org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeter
    org.broadinstitute.hellbender.utils.nio.org.broadinstitute.hellbender.utils.nio.NioFileCopierWithProgressMeterResults
    org.broadinstitute.hellbender.utils.nio.org.broadinstitute.hellbender.utils.nio.PathLineIterator
    org.broadinstitute.hellbender.utils.pairhmm
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.DragstrReadSTRAnalyzer
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.FlowBasedPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.Log10PairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.LoglessPDPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.LoglessPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.N2MemoryPDPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.N2MemoryPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.PDPairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.PairHMM
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputation
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.PairHMMModel
    org.broadinstitute.hellbender.utils.pairhmm.org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM
    org.broadinstitute.hellbender.utils.param
    org.broadinstitute.hellbender.utils.param.org.broadinstitute.hellbender.utils.param.ParamUtils
    org.broadinstitute.hellbender.utils.pileup
    org.broadinstitute.hellbender.utils.pileup.org.broadinstitute.hellbender.utils.pileup.PileupBasedAlleles
    org.broadinstitute.hellbender.utils.pileup.org.broadinstitute.hellbender.utils.pileup.PileupElement
    org.broadinstitute.hellbender.utils.pileup.org.broadinstitute.hellbender.utils.pileup.ReadPileup
    org.broadinstitute.hellbender.utils.python
    org.broadinstitute.hellbender.utils.python.org.broadinstitute.hellbender.utils.python.PythonExecutorBase
    org.broadinstitute.hellbender.utils.python.org.broadinstitute.hellbender.utils.python.PythonScriptExecutor
    org.broadinstitute.hellbender.utils.python.org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException
    org.broadinstitute.hellbender.utils.python.org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor
    org.broadinstitute.hellbender.utils.read
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.AlignmentUtils
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ArtificialBAMBuilder
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ArtificialReadIterator
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ArtificialReadUtils
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.CigarBuilder
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.CigarUtils
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.FlowBasedKeyCodec
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.FlowBasedRead
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.FlowBasedReadUtils
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.Fragment
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.GATKRead
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.GATKReadWriter
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.HeaderlessSAMRecordCoordinateComparator
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.PrimaryAlignmentKey
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ReadConstants
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ReadCoordinateComparator
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ReadQueryNameComparator
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ReadUtils
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.ReadsWriteFormat
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter
    org.broadinstitute.hellbender.utils.read.org.broadinstitute.hellbender.utils.read.SAMRecordToGATKReadAdapter
    org.broadinstitute.hellbender.utils.read.markduplicates
    org.broadinstitute.hellbender.utils.read.markduplicates.org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics
    org.broadinstitute.hellbender.utils.read.markduplicates.org.broadinstitute.hellbender.utils.read.markduplicates.LibraryIdGenerator
    org.broadinstitute.hellbender.utils.read.markduplicates.org.broadinstitute.hellbender.utils.read.markduplicates.MarkDuplicatesScoringStrategy
    org.broadinstitute.hellbender.utils.read.markduplicates.org.broadinstitute.hellbender.utils.read.markduplicates.ReadsKey
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.EmptyFragment
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.FlowModeFragment
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Fragment
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.MarkDuplicatesSparkRecord
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Pair
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.PairedEnds
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.Passthrough
    org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords.TransientFieldPhysicalLocation
    org.broadinstitute.hellbender.utils.read.mergealignment
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.AbstractAlignmentMerger
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.BestMapqPrimaryAlignmentSelectionStrategy
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.EarliestFragmentPrimaryAlignmentSelectionStrategy
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.HitsForInsert
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.MostDistantPrimaryAlignmentSelectionStrategy
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.PrimaryAlignmentSelectionStrategy
    org.broadinstitute.hellbender.utils.read.mergealignment.org.broadinstitute.hellbender.utils.read.mergealignment.SamAlignmentMerger
    org.broadinstitute.hellbender.utils.recalibration
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.BQSR.R
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.EventType
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.QualQuantizer
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.QuantizationInfo
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.ReadRecalibrationInfo
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.RecalDatum
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.RecalUtils
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport
    org.broadinstitute.hellbender.utils.recalibration.org.broadinstitute.hellbender.utils.recalibration.RecalibrationTables
    org.broadinstitute.hellbender.utils.recalibration.covariates
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.ContextCovariate
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.Covariate
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.CovariateKeyCache
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.CycleCovariate
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.QualityScoreCovariate
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.ReadCovariates
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.ReadGroupCovariate
    org.broadinstitute.hellbender.utils.recalibration.covariates.org.broadinstitute.hellbender.utils.recalibration.covariates.StandardCovariateList
    org.broadinstitute.hellbender.utils.reference
    org.broadinstitute.hellbender.utils.reference.org.broadinstitute.hellbender.utils.reference.AbsoluteCoordinates
    org.broadinstitute.hellbender.utils.reference.org.broadinstitute.hellbender.utils.reference.ReferenceBases
    org.broadinstitute.hellbender.utils.reference.org.broadinstitute.hellbender.utils.reference.ReferenceUtils
    org.broadinstitute.hellbender.utils.reference.org.broadinstitute.hellbender.utils.reference.TwoBitReference
    org.broadinstitute.hellbender.utils.report
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReport
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReportColumn
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReportColumnFormat
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReportDataType
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReportTable
    org.broadinstitute.hellbender.utils.report.org.broadinstitute.hellbender.utils.report.GATKReportVersion
    org.broadinstitute.hellbender.utils.runtime
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.AsynchronousStreamWriter
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutput
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.CapturedStreamOutputSnapshot
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.InputStreamSettings
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.OutputStreamSettings
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProcessController
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProcessControllerAckResult
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProcessControllerBase
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProcessOutput
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProcessSettings
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ProgressLogger
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.RuntimeUtils
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ScriptExecutor
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.ScriptExecutorException
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.StreamLocation
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.StreamOutput
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.StreamingProcessController
    org.broadinstitute.hellbender.utils.runtime.org.broadinstitute.hellbender.utils.runtime.StreamingToolConstants
    org.broadinstitute.hellbender.utils.samples
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.Affection
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.MendelianViolation
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.PedReader
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.PedigreeValidationType
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.Sample
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.SampleDB
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.SampleDBBuilder
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.Sex
    org.broadinstitute.hellbender.utils.samples.org.broadinstitute.hellbender.utils.samples.Trio
    org.broadinstitute.hellbender.utils.smithwaterman
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SWNativeAlignerWrapper
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignment
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAlignmentConstants
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAligner
    org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner
    org.broadinstitute.hellbender.utils.spark
    org.broadinstitute.hellbender.utils.spark.org.broadinstitute.hellbender.utils.spark.JoinReadsWithVariants
    org.broadinstitute.hellbender.utils.spark.org.broadinstitute.hellbender.utils.spark.SparkConverter
    org.broadinstitute.hellbender.utils.spark.org.broadinstitute.hellbender.utils.spark.SparkUtils
    org.broadinstitute.hellbender.utils.svd
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.ApacheSingularValueDecomposer
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.OjAlgoSingularValueDecomposer
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.SVD
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.SVDFactory
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.SimpleSVD
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.SingularValueDecomposer
    org.broadinstitute.hellbender.utils.svd.org.broadinstitute.hellbender.utils.svd.SparkSingularValueDecomposer
    org.broadinstitute.hellbender.utils.text
    org.broadinstitute.hellbender.utils.text.org.broadinstitute.hellbender.utils.text.TextFormattingUtils
    org.broadinstitute.hellbender.utils.text.org.broadinstitute.hellbender.utils.text.XReadLines
    org.broadinstitute.hellbender.utils.tsv
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.DataLine
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.TableColumnCollection
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.TableReader
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.TableUtils
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.TableWriter
    org.broadinstitute.hellbender.utils.tsv.org.broadinstitute.hellbender.utils.tsv.package-info
    org.broadinstitute.hellbender.utils.variant
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.DbSnpBitSetUtil
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.DbSnpVariantType
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKSVVariantContextUtils
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKVCFConstants
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKVCFIndexType
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKVariant
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.MinimalVariant
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.VariantContextGetters
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.VariantContextVariantAdapter
    org.broadinstitute.hellbender.utils.variant.org.broadinstitute.hellbender.utils.variant.VcfUtils
    org.broadinstitute.hellbender.utils.variant.writers
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.GVCFBlock
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiningIterator
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.GVCFWriter
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.HomRefBlock
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.IntervalFilteringVcfWriter
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFWriter
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.ReblockingOptions
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.ShardingVCFWriter
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFWriter
    org.broadinstitute.hellbender.utils.variant.writers.org.broadinstitute.hellbender.utils.variant.writers.TLODBlock
    org.broadinstitute.hellbender.utils.wdlTemplates
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.common.html
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlIndexTemplate.html.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlJSONTemplate.json.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlJSONTemplateAllArgs.json.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlJSONTemplateAllArgsTest.json.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlToolTemplate.wdl.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlToolTemplateAllArgs.wdl.ftl
    org.broadinstitute.hellbender.utils.wdlTemplates.org.broadinstitute.hellbender.utils.wdlTemplates.wdlToolTemplateAllArgsTest.wdl.ftl




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