Hierarchy For Package org.broadinstitute.hellbender.engine

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval (implements htsjdk.samtools.util.Locatable)
  • org.broadinstitute.hellbender.engine.ActivityProfileStateIterator (implements java.util.Iterator<E>)
  • org.broadinstitute.hellbender.engine.AlignmentContext (implements org.broadinstitute.hellbender.utils.HasGenomeLocation, htsjdk.samtools.util.Locatable)
  • org.broadinstitute.hellbender.engine.AssemblyRegion (implements htsjdk.samtools.util.Locatable)
  • org.broadinstitute.hellbender.engine.AssemblyRegionFromActivityProfileStateIterator (implements java.util.Iterator<E>)
  • org.broadinstitute.hellbender.engine.AssemblyRegionIterator (implements java.util.Iterator<E>)
  • org.apache.commons.pool.BaseObjectPool<T> (implements org.apache.commons.pool.ObjectPool<T>)
    • org.apache.commons.pool.impl.GenericObjectPool<T> (implements org.apache.commons.pool.ObjectPool<T>)
      • org.broadinstitute.hellbender.engine.ReadsDataSourcePool (implements java.lang.AutoCloseable)
  • org.broadinstitute.hellbender.cmdline.CommandLineProgram (implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
    • org.broadinstitute.hellbender.engine.GATKTool
      • org.broadinstitute.hellbender.engine.WalkerBase
        • org.broadinstitute.hellbender.engine.AbstractConcordanceWalker
        • org.broadinstitute.hellbender.engine.AssemblyRegionWalker
        • org.broadinstitute.hellbender.engine.FeatureWalker<F>
        • org.broadinstitute.hellbender.engine.IntervalWalker
        • org.broadinstitute.hellbender.engine.LocusWalker
          • org.broadinstitute.hellbender.engine.LocusWalkerByInterval
        • org.broadinstitute.hellbender.engine.ReadWalker
          • org.broadinstitute.hellbender.engine.DuplicateSetWalker
          • org.broadinstitute.hellbender.engine.MultiplePassReadWalker
        • org.broadinstitute.hellbender.engine.ReferenceWalker
        • org.broadinstitute.hellbender.engine.VariantWalkerBase
          • org.broadinstitute.hellbender.engine.MultiVariantWalker
            • org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart
          • org.broadinstitute.hellbender.engine.VariantLocusWalker
          • org.broadinstitute.hellbender.engine.VariantWalker
            • org.broadinstitute.hellbender.engine.MultiplePassVariantWalker
              • org.broadinstitute.hellbender.engine.TwoPassVariantWalker
  • org.broadinstitute.hellbender.engine.FeatureContext
  • org.broadinstitute.hellbender.engine.FeatureDataSource<T> (implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.GATKDataSource<T>)
  • org.broadinstitute.hellbender.engine.FeatureManager (implements java.lang.AutoCloseable)
  • htsjdk.io.HtsPath (implements htsjdk.io.IOPath, java.io.Serializable)
    • org.broadinstitute.hellbender.engine.GATKPath (implements java.io.Serializable, org.broadinstitute.barclay.argparser.TaggedArgument)
      • org.broadinstitute.hellbender.engine.FeatureInput<T> (implements java.io.Serializable)
  • org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard (implements org.broadinstitute.hellbender.engine.MultiIntervalShard<T>)
  • org.broadinstitute.hellbender.engine.MultiVariantDataSource (implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.GATKDataSource<T>)
  • org.broadinstitute.hellbender.engine.ProgressMeter
  • org.broadinstitute.hellbender.engine.ReadContextData (implements java.io.Serializable)
  • org.broadinstitute.hellbender.engine.ReadsContext (implements java.lang.Iterable<T>)
  • org.broadinstitute.hellbender.engine.ReadsPathDataSource (implements org.broadinstitute.hellbender.engine.ReadsDataSource)
  • org.broadinstitute.hellbender.engine.ReferenceContext (implements org.broadinstitute.hellbender.engine.BasicReference, java.lang.Iterable<T>, htsjdk.samtools.util.Locatable)
  • org.broadinstitute.hellbender.engine.ReferenceFileSource (implements org.broadinstitute.hellbender.engine.ReferenceDataSource)
  • org.broadinstitute.hellbender.engine.ReferenceMemorySource (implements org.broadinstitute.hellbender.engine.ReferenceDataSource)
  • org.broadinstitute.hellbender.engine.ReferenceShard (implements java.io.Serializable)
  • org.broadinstitute.hellbender.engine.ShardBoundary (implements htsjdk.samtools.util.Locatable, java.io.Serializable)
    • org.broadinstitute.hellbender.engine.ReadlessAssemblyRegion
  • org.broadinstitute.hellbender.engine.ShardBoundaryShard<T> (implements java.io.Serializable, org.broadinstitute.hellbender.engine.Shard<T>)
  • org.broadinstitute.hellbender.engine.ShardToMultiIntervalShardAdapter<T> (implements org.broadinstitute.hellbender.engine.MultiIntervalShard<T>, java.io.Serializable, org.broadinstitute.hellbender.engine.Shard<T>)
  • org.broadinstitute.hellbender.engine.TraversalParameters (implements java.io.Serializable)
  • org.broadinstitute.hellbender.engine.VariantShard

Interface Hierarchy

• org.broadinstitute.hellbender.engine.AssemblyRegionEvaluator
• java.lang.AutoCloseable
  • org.broadinstitute.hellbender.engine.ReadsDataSource (also extends org.broadinstitute.hellbender.engine.GATKDataSource<T>)
  • org.broadinstitute.hellbender.engine.ReferenceDataSource (also extends org.broadinstitute.hellbender.engine.GATKDataSource<T>)
• org.broadinstitute.hellbender.engine.BasicReference
• java.lang.Iterable<T>
  • org.broadinstitute.hellbender.engine.GATKDataSource<T>
    • org.broadinstitute.hellbender.engine.ReadsDataSource (also extends java.lang.AutoCloseable)
    • org.broadinstitute.hellbender.engine.ReferenceDataSource (also extends java.lang.AutoCloseable)
  • org.broadinstitute.hellbender.engine.MultiIntervalShard<T>
  • org.broadinstitute.hellbender.engine.Shard<T> (also extends htsjdk.samtools.util.Locatable)
• htsjdk.samtools.util.Locatable
  • org.broadinstitute.hellbender.engine.Shard<T> (also extends java.lang.Iterable<T>)
• org.broadinstitute.hellbender.engine.MultiplePassReadWalker.GATKReadConsumer

Annotation Type Hierarchy

• org.broadinstitute.hellbender.engine.DoNotSubclass (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.broadinstitute.hellbender.engine.AlignmentContext.ReadOrientation