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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.
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.
AssemblyRegionIterator
(implements java.util.Iterator<E>)
org.broadinstitute.hellbender.cmdline.
CommandLineProgram
(implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
org.broadinstitute.hellbender.engine.
GATKTool
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.
ReadWalker
org.broadinstitute.hellbender.engine.
TwoPassReadWalker
org.broadinstitute.hellbender.engine.
VariantWalkerBase
org.broadinstitute.hellbender.engine.
MultiVariantWalker
org.broadinstitute.hellbender.engine.
MultiVariantWalkerGroupedOnStart
org.broadinstitute.hellbender.engine.
VariantWalker
org.broadinstitute.hellbender.engine.
TwoPassVariantWalker
org.broadinstitute.hellbender.engine.
ContextShard
(implements java.io.Serializable)
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.
FeatureInput
<T> (implements java.io.Serializable)
org.broadinstitute.hellbender.engine.
FeatureManager
(implements java.lang.AutoCloseable)
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.
ReadsDataSource
(implements java.lang.AutoCloseable, org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
org.broadinstitute.hellbender.engine.
ReferenceContext
(implements java.lang.Iterable<T>)
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.
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.
ReferenceDataSource
(also extends org.broadinstitute.hellbender.engine.
GATKDataSource
<T>)
java.lang.Iterable<T>
org.broadinstitute.hellbender.engine.
GATKDataSource
<T>
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>)
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
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