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Download gatk JAR 4.1.4.0 with all dependencies


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Files of the artifact gatk version 4.1.4.0 from the group org.broadinstitute.

Artifact gatk
Group org.broadinstitute
Version 4.1.4.0
Last update 16. October 2019
Tags: development gatk
Organization not specified
URL http://github.com/broadinstitute/gatk
License BSD 3-Clause
Dependencies amount 48
Dependencies barclay, owner, picard, genomicsdb, opencsv, guava, htsjdk, google-cloud-nio, gov.nist.math.jama, gcs-connector, log4j-api, log4j-core, log4j-jcl, commons-lang3, commons-math3, commons-collections4, commons-vfs2, commons-configuration2, commons-beanutils, commons-io, reflections, fastutil, hdf5-java-bindings, gatk-native-bindings, ojalgo, ojalgo-commons-math3, spark-mllib_2.11, paranamer, bdg-formats, adam-core-spark2_2.11, jgrapht-core, disq, 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, xgboost-predictor, natural-comparator, objenesis,
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Source code of gatk version 4.1.4.0

META-INF
META-INF.META-INF.MANIFEST.MF
htsjdk.samtools
htsjdk.samtools.htsjdk.samtools.SAMRecordSparkCodec
large.cnn_score_variants
large.cnn_score_variants.large.cnn_score_variants.1d_cnn_mix_train_full_bn.hd5
large.cnn_score_variants.large.cnn_score_variants.1d_cnn_mix_train_full_bn.json
large.cnn_score_variants.large.cnn_score_variants.2d_cnn_mix_train.hd5
large.cnn_score_variants.large.cnn_score_variants.2d_cnn_mix_train.json
large.cnn_score_variants.large.cnn_score_variants.small_2d.hd5
large.cnn_score_variants.large.cnn_score_variants.small_2d.json
large
large.large.sv_evidence_classifier.bin
large.large.testResourceFile.txt
.log4j.properties
.log4j2.xml
org.broadinstitute.hellbender
org.broadinstitute.hellbender.org.broadinstitute.hellbender.Main
org.broadinstitute.hellbender.cmdline
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.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.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.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.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.DoNotSubclass
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.GATKPathSpecifier
org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.GATKTool
org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.GenomicsDBBCFCodec
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.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.MultiVariantWalkerGroupedOnStart
org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.PathSpecifier
org.broadinstitute.hellbender.engine.org.broadinstitute.hellbender.engine.PathURI
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.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.TwoPassReadWalker
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.FragmentLengthReadFilter
org.broadinstitute.hellbender.engine.filters.org.broadinstitute.hellbender.engine.filters.IntervalOverlapReadFilter
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.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.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.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.JsonSerializer
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.DirectFullByteArrayByteAccess
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.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.AnnotatePairOrientation
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.ApplyBQSRArgumentCollection
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.ApplyBQSRUniqueArgumentCollection
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.BwaMemIndexImageCreator
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.ClipReads
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.CompareIntervalLists
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.ConvertHeaderlessHadoopBamShardToBam
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.CountBases
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.CountReads
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.DownsampleableSparkReadShard
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.FixCallSetSampleOrdering
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.FixMisencodedBaseQualityReads
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.FlagStat
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.GatherVcfsCloud
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.GetSampleName
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.HaplotypeCallerSpark
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.IndexFeatureFile
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.LeftAlignIndels
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.PrintBGZFBlockInformation
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.PrintReads
org.broadinstitute.hellbender.tools.org.broadinstitute.hellbender.tools.SplitReads
org.broadinstitute.hellbender.tools.copynumber
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
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
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.ModelSegments
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
org.broadinstitute.hellbender.tools.copynumber.arguments
org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberArgumentValidationUtils
org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument
org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCNVHybridADVIArgumentCollection
org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineCallingArgumentCollection
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
org.broadinstitute.hellbender.tools.copynumber.arguments.org.broadinstitute.hellbender.tools.copynumber.arguments.HybridADVIArgumentCollection
org.broadinstitute.hellbender.tools.copynumber.caller
org.broadinstitute.hellbender.tools.copynumber.caller.org.broadinstitute.hellbender.tools.copynumber.caller.SimpleCopyRatioCaller
org.broadinstitute.hellbender.tools.copynumber
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.case_denoising_calling.py
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
org.broadinstitute.hellbender.tools.copynumber.datacollection
org.broadinstitute.hellbender.tools.copynumber.datacollection.org.broadinstitute.hellbender.tools.copynumber.datacollection.AllelicCountCollector
org.broadinstitute.hellbender.tools.copynumber.denoising
org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.GCBiasCorrector
org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.HDF5SVDReadCountPanelOfNormals
org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisedCopyRatioResult
org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.SVDDenoisingUtils
org.broadinstitute.hellbender.tools.copynumber.denoising.org.broadinstitute.hellbender.tools.copynumber.denoising.SVDReadCountPanelOfNormals
org.broadinstitute.hellbender.tools.copynumber.formats
org.broadinstitute.hellbender.tools.copynumber.formats.org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils
org.broadinstitute.hellbender.tools.copynumber.formats.collections
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractLocatableCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractRecordCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleLocatableCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AbstractSampleRecordCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AlleleFractionSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AllelicCountCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.AnnotatedIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.BaselineCopyNumberCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledCopyRatioSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CalledLegacySegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyNumberPosteriorDistributionCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CopyRatioSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.CoveragePerContigCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.HDF5SimpleCountCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.IntegerCopyNumberSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.LegacySegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.LinearCopyRatioCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.ModeledSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.MultidimensionalSegmentCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.NonLocatableDoubleCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.ParameterDecileCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleCountCollection
org.broadinstitute.hellbender.tools.copynumber.formats.collections.org.broadinstitute.hellbender.tools.copynumber.formats.collections.SimpleIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.formats.metadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.Metadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.MetadataUtils
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleLocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleLocatableMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.metadata.org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SimpleSampleMetadata
org.broadinstitute.hellbender.tools.copynumber.formats.records
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.AlleleFractionSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.AllelicCount
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyNumberPosteriorDistribution
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatio
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CopyRatioSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.CoveragePerContig
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.IntegerCopyNumberSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.IntervalCopyNumberGenotypingData
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.LegacySegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.LinearCopyRatio
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.ModeledSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.MultidimensionalSegment
org.broadinstitute.hellbender.tools.copynumber.formats.records.org.broadinstitute.hellbender.tools.copynumber.formats.records.SimpleCount
org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
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org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap
org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations
org.broadinstitute.hellbender.tools.copynumber.gcnv
org.broadinstitute.hellbender.tools.copynumber.gcnv.org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVIntervalVariantComposer
org.broadinstitute.hellbender.tools.copynumber.gcnv.org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVNamingConstants
org.broadinstitute.hellbender.tools.copynumber.gcnv.org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVSegmentVariantComposer
org.broadinstitute.hellbender.tools.copynumber.gcnv.org.broadinstitute.hellbender.tools.copynumber.gcnv.GermlineCNVVariantComposer
org.broadinstitute.hellbender.tools.copynumber.gcnv.org.broadinstitute.hellbender.tools.copynumber.gcnv.IntegerCopyNumberState
org.broadinstitute.hellbender.tools.copynumber.models
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionGlobalParameters
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionInitializer
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionLikelihoods
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionModeller
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionParameter
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionPrior
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionSamplers
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionSegmentedData
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.AlleleFractionState
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioModeller
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioParameter
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioSamplers
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioSegmentedData
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.CopyRatioState
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.FunctionCache
org.broadinstitute.hellbender.tools.copynumber.models.org.broadinstitute.hellbender.tools.copynumber.models.MultidimensionalModeller
org.broadinstitute.hellbender.tools.copynumber.plotting
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.CNVPlottingLibrary.R
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios.R
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments.R
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.PlotModeledSegments
org.broadinstitute.hellbender.tools.copynumber.plotting.org.broadinstitute.hellbender.tools.copynumber.plotting.PlottingUtils
org.broadinstitute.hellbender.tools.copynumber
org.broadinstitute.hellbender.tools.copynumber.org.broadinstitute.hellbender.tools.copynumber.segment_gcnv_calls.py
org.broadinstitute.hellbender.tools.copynumber.segmentation
org.broadinstitute.hellbender.tools.copynumber.segmentation.org.broadinstitute.hellbender.tools.copynumber.segmentation.AlleleFractionKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.segmentation.org.broadinstitute.hellbender.tools.copynumber.segmentation.CopyRatioKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.segmentation.org.broadinstitute.hellbender.tools.copynumber.segmentation.MultidimensionalKernelSegmenter
org.broadinstitute.hellbender.tools.copynumber.utils
org.broadinstitute.hellbender.tools.copynumber.utils.org.broadinstitute.hellbender.tools.copynumber.utils.CombineSegmentBreakpoints
org.broadinstitute.hellbender.tools.copynumber.utils.org.broadinstitute.hellbender.tools.copynumber.utils.HDF5Utils
org.broadinstitute.hellbender.tools.copynumber.utils.org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegions
org.broadinstitute.hellbender.tools.copynumber.utils.org.broadinstitute.hellbender.tools.copynumber.utils.MergeAnnotatedRegionsByAnnotation
org.broadinstitute.hellbender.tools.copynumber.utils.org.broadinstitute.hellbender.tools.copynumber.utils.TagGermlineEvents
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedInterval
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalCollection
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalHeader
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalUtils
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.AnnotatedIntervalWriter
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.SimpleAnnotatedIntervalWriter
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval.annotated_region_default.config
org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging.SimpleGermlineTagger
org.broadinstitute.hellbender.tools.copynumber.utils.optimization
org.broadinstitute.hellbender.tools.copynumber.utils.optimization.org.broadinstitute.hellbender.tools.copynumber.utils.optimization.PersistenceOptimizer
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.org.broadinstitute.hellbender.tools.copynumber.utils.segmentation.KernelSegmenter
org.broadinstitute.hellbender.tools.examples
org.broadinstitute.hellbender.tools.examples.org.broadinstitute.hellbender.tools.examples.ExampleAssemblyRegionWalker
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.ExampleNioCountReads
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.exome
org.broadinstitute.hellbender.tools.exome.org.broadinstitute.hellbender.tools.exome.FilterByOrientationBias
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.ArtifactStatisticsScorer
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationBiasFilterConstants
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationBiasFilterSummaryTableColumn
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationBiasFilterer
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationBiasUtils
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.OrientationSampleTransitionSummary
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.PreAdapterOrientationScorer
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
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org.broadinstitute.hellbender.tools.spark.transforms
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org.broadinstitute.hellbender.tools.validation.org.broadinstitute.hellbender.tools.validation.validate-reads-spark-pipeline.sh
org.broadinstitute.hellbender.tools.walkers
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org.broadinstitute.hellbender.tools.walkers.annotator
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org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
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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
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.GenotypeLikelihoodCalculators
org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel
org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingData
org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine
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.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
org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.OutputMode
org.broadinstitute.hellbender.tools.walkers.genotyper.org.broadinstitute.hellbender.tools.walkers.genotyper.PloidyModel
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
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFPriorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.CustomAFPriorProvider
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.HeterozygosityAFPriorProvider
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.haplotypecaller
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.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.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.LocationAndAlleles
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.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.RandomLikelihoodCalculationEngine
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.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.GraphUtils
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.readthreading
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.haplotypecaller.readthreading.org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.TestingReadThreadingGraph
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.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.MutectStats
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.SequencingError
org.broadinstitute.hellbender.tools.walkers.mutect.clustering.org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel
org.broadinstitute.hellbender.tools.walkers.mutect.filtering
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.ChimericOriginalAlignmentFilter
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.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.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.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.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.PolymorphicNuMTFilter
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.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.OverhangFixingManager
org.broadinstitute.hellbender.tools.walkers.rnaseq.org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads
org.broadinstitute.hellbender.tools.walkers.validation
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.AnnotateVcfWithBamDepth
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
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.Concordance
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceState
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.ConcordanceSummaryRecord
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.CountFalsePositives
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
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.MixingFraction
org.broadinstitute.hellbender.tools.walkers.validation.org.broadinstitute.hellbender.tools.walkers.validation.RemoveNearbyIndels
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter
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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.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.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
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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
org.broadinstitute.hellbender.tools.walkers.varianteval.org.broadinstitute.hellbender.tools.walkers.varianteval.plotAlleleFrequencyQC.R
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
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org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.AlleleFrequency
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.CompFeatureInput
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org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Filter
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org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.IntervalStratification
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.JexlExpression
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Novelty
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.RequiredStratification
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.Sample
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org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.StandardStratification
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.TandemRepeat
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantType
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
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org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager.Stratifier
org.broadinstitute.hellbender.tools.walkers.varianteval.util
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org.broadinstitute.hellbender.tools.walkers.varianteval.util.org.broadinstitute.hellbender.tools.walkers.varianteval.util.Molten
org.broadinstitute.hellbender.tools.walkers.varianteval.util.org.broadinstitute.hellbender.tools.walkers.varianteval.util.SnpEffUtil
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org.broadinstitute.hellbender.tools.walkers.variantutils
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org.broadinstitute.hellbender.tools.walkers.variantutils.org.broadinstitute.hellbender.tools.walkers.variantutils.FamilyLikelihoods
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org.broadinstitute.hellbender.tools.walkers.variantutils.org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants
org.broadinstitute.hellbender.tools.walkers.variantutils.org.broadinstitute.hellbender.tools.walkers.variantutils.UpdateVCFSequenceDictionary
org.broadinstitute.hellbender.tools.walkers.variantutils.org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants
org.broadinstitute.hellbender.tools.walkers.variantutils.org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable
org.broadinstitute.hellbender.tools.walkers.vqsr
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org.broadinstitute.hellbender.tools.walkers.vqsr.org.broadinstitute.hellbender.tools.walkers.vqsr.TruthSensitivityTranche
org.broadinstitute.hellbender.tools.walkers.vqsr.org.broadinstitute.hellbender.tools.walkers.vqsr.VQSLODTranche
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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.org.broadinstitute.hellbender.tools.walkers.vqsr.training.py
org.broadinstitute.hellbender.transformers
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.AdapterTrimTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.BQSRReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.BaseQualityClipReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.BaseQualityReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.DUSTReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.MappingQualityReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.MisencodedBaseQualityReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.NDNCigarReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.PalindromeArtifactClipReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.ReadTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.SimpleRepeatMaskTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.StripMateNumberTransformer
org.broadinstitute.hellbender.transformers.org.broadinstitute.hellbender.transformers.VariantTransformer
org.broadinstitute.hellbender.utils
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org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.ClassUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.CompressedDataList
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.DigammaCache
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Dirichlet
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.FisherExactTest
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GATKProtectedVariantContextUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenomeLoc
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenomeLocParser
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenomeLocSortedSet
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenotypeCounts
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.GenotypeUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.HasGenomeLocation
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Histogram
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IGVUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IndexRange
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IndexUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IntToDoubleFunctionCache
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IntegrationUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IntervalMergingRule
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IntervalSetRule
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.IntervalUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.KV
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.LRUCache
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Log10Cache
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Log10FactorialCache
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.LoggingUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.MRUCachingSAMSequenceDictionary
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.MannWhitneyU
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.MathUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.MatrixSummaryUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.NGSPlatform
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.NativeUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.NaturalLogUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Nucleotide
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.OptimizationUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.QualityUtils
org.broadinstitute.hellbender.utils.R
org.broadinstitute.hellbender.utils.R.org.broadinstitute.hellbender.utils.R.RScriptExecutor
org.broadinstitute.hellbender.utils.R.org.broadinstitute.hellbender.utils.R.RScriptExecutorException
org.broadinstitute.hellbender.utils.R.org.broadinstitute.hellbender.utils.R.RScriptLibrary
org.broadinstitute.hellbender.utils.R.org.broadinstitute.hellbender.utils.R.gsalib.tar.gz
org.broadinstitute.hellbender.utils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SATagBuilder
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SequenceDictionaryUtils
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SequencerFlowClass
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SerializableFunction
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SimpleInterval
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Trilean
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.UniqueIDWrapper
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.UnsignedTypeUtil
org.broadinstitute.hellbender.utils.org.broadinstitute.hellbender.utils.Utils
org.broadinstitute.hellbender.utils.activityprofile
org.broadinstitute.hellbender.utils.activityprofile.org.broadinstitute.hellbender.utils.activityprofile.ActivityProfile
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org.broadinstitute.hellbender.utils.artifacts
org.broadinstitute.hellbender.utils.artifacts.org.broadinstitute.hellbender.utils.artifacts.Transition
org.broadinstitute.hellbender.utils.baq
org.broadinstitute.hellbender.utils.baq.org.broadinstitute.hellbender.utils.baq.BAQ
org.broadinstitute.hellbender.utils.bwa
org.broadinstitute.hellbender.utils.bwa.org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils
org.broadinstitute.hellbender.utils.bwa.org.broadinstitute.hellbender.utils.bwa.BwaMemIndexCache
org.broadinstitute.hellbender.utils.clipping
org.broadinstitute.hellbender.utils.clipping.org.broadinstitute.hellbender.utils.clipping.ClippingOp
org.broadinstitute.hellbender.utils.clipping.org.broadinstitute.hellbender.utils.clipping.ClippingRepresentation
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org.broadinstitute.hellbender.utils.codecs
org.broadinstitute.hellbender.utils.codecs.org.broadinstitute.hellbender.utils.codecs.AnnotatedIntervalCodec
org.broadinstitute.hellbender.utils.codecs.org.broadinstitute.hellbender.utils.codecs.LineIteratorReader
org.broadinstitute.hellbender.utils.codecs.org.broadinstitute.hellbender.utils.codecs.ProgressReportingDelegatingCodec
org.broadinstitute.hellbender.utils.codecs.gencode
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCDSFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfCodec
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfExonFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfFeatureBaseData
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfGeneFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfSelenocysteineFeature
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org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfStopCodonFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfTranscriptFeature
org.broadinstitute.hellbender.utils.codecs.gencode.org.broadinstitute.hellbender.utils.codecs.gencode.GencodeGtfUTRFeature
org.broadinstitute.hellbender.utils.codecs.sampileup
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org.broadinstitute.hellbender.utils.codecs.sampileup.org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupElement
org.broadinstitute.hellbender.utils.codecs.sampileup.org.broadinstitute.hellbender.utils.codecs.sampileup.SAMPileupFeature
org.broadinstitute.hellbender.utils.codecs.table
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org.broadinstitute.hellbender.utils.codecs.table.org.broadinstitute.hellbender.utils.codecs.table.TableFeature
org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
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org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable.XsvTableFeature
org.broadinstitute.hellbender.utils.collections
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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.SmithWatermanIntelAligner
org.broadinstitute.hellbender.utils.smithwaterman.org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner
org.broadinstitute.hellbender.utils.solver
org.broadinstitute.hellbender.utils.solver.org.broadinstitute.hellbender.utils.solver.RobustBrentSolver
org.broadinstitute.hellbender.utils.solver.org.broadinstitute.hellbender.utils.solver.SynchronizedUnivariateSolver
org.broadinstitute.hellbender.utils.solver.org.broadinstitute.hellbender.utils.solver.UnivariateSolverJobDescription
org.broadinstitute.hellbender.utils.solver.org.broadinstitute.hellbender.utils.solver.UnivariateSolverSpecifications
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.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.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.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




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