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Hierarchy For Package org.broadinstitute.hellbender.tools
Package Hierarchies:
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Class Hierarchy
java.lang.Object
org.broadinstitute.hellbender.tools.
ApplyBQSRUniqueArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.
ApplyBQSRArgumentCollection
org.broadinstitute.hellbender.tools.
ClipReads.ClippingData
org.broadinstitute.hellbender.cmdline.
CommandLineProgram
(implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
org.broadinstitute.hellbender.tools.
BwaMemIndexImageCreator
org.broadinstitute.hellbender.tools.
ConvertHeaderlessHadoopBamShardToBam
org.broadinstitute.hellbender.tools.
GatherVcfsCloud
org.broadinstitute.hellbender.engine.
GATKTool
org.broadinstitute.hellbender.tools.
GetSampleName
org.broadinstitute.hellbender.engine.
ReadWalker
org.broadinstitute.hellbender.tools.
ClipReads
org.broadinstitute.hellbender.tools.
CountBases
org.broadinstitute.hellbender.tools.
CountReads
org.broadinstitute.hellbender.tools.
FixMisencodedBaseQualityReads
org.broadinstitute.hellbender.tools.
FlagStat
org.broadinstitute.hellbender.tools.
LeftAlignIndels
org.broadinstitute.hellbender.tools.
PrintReads
org.broadinstitute.hellbender.tools.
SplitReads
org.broadinstitute.hellbender.engine.
VariantWalkerBase
org.broadinstitute.hellbender.engine.
VariantWalker
org.broadinstitute.hellbender.tools.
AnnotatePairOrientation
org.broadinstitute.hellbender.tools.
FixCallSetSampleOrdering
org.broadinstitute.hellbender.tools.
IndexFeatureFile
org.broadinstitute.hellbender.engine.spark.
SparkCommandLineProgram
(implements java.io.Serializable)
org.broadinstitute.hellbender.engine.spark.
GATKSparkTool
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark
org.broadinstitute.hellbender.tools.
DownsampleableSparkReadShard
(implements java.io.Serializable, org.broadinstitute.hellbender.engine.
Shard
<T>)
org.broadinstitute.hellbender.tools.
FlagStat.FlagStatus
(implements java.io.Serializable)
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark.ReferenceMultiSourceAdapter
(implements org.broadinstitute.hellbender.engine.
ReferenceDataSource
, htsjdk.samtools.reference.ReferenceSequenceFile, java.io.Serializable)
org.broadinstitute.hellbender.tools.
HaplotypeCallerSpark.ShardingArgumentCollection
(implements java.io.Serializable)
org.broadinstitute.hellbender.utils.clipping.
ReadClipper
org.broadinstitute.hellbender.tools.
ClipReads.ReadClipperWithData
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.broadinstitute.hellbender.tools.
GatherVcfsCloud.GatherType
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