Hierarchy For Package org.broadinstitute.hellbender.tools.spark.sv.evidence

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointDensityFilter (implements java.util.Iterator<E>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence
      • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.DiscordantReadPairEvidence
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize
      • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel
      • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped
      • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidenceClusterer (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.cmdline.CommandLineProgram (implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
    • org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram (implements java.io.Serializable)
      • org.broadinstitute.hellbender.engine.spark.GATKSparkTool
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.CalcMetadataSpark
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.ExtractSVEvidenceSpark
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark
        • org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLinkClusterer
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.AssembledEvidenceResults
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBreakpointEvidenceSpark.IntPair
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.IntervalCoverageFinder (implements java.lang.Iterable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCleaner (implements java.lang.Iterable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerCounter
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.KSWindowFinder
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.PartitionCrossingChecker
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval (implements java.util.Map.Entry<K,V>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameFinder (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameIntervalFinder (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameKmerizer (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNamesForKmersFinder (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadClassifier (implements java.util.function.Function<T,R>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadsForQNamesFinder (implements java.lang.Iterable<T>)
  • com.esotericsoftware.kryo.Serializer<T>
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ExternalEvidence.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.InterContigPair.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.LargeIndel.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.MateUnmapped.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.OutiesPair.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.ReadEvidence.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SameStrandPair.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.SplitRead.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.TemplateSizeAnomaly.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.BreakpointEvidence.WeirdTemplateSize.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.EvidenceTargetLink.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.LibraryStatistics.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.QNameAndInterval.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.LibraryRawStatistics.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionBounds.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.PartitionStatistics.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.ReadMetadata.Serializer
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong (implements java.lang.Comparable<T>)
      • org.broadinstitute.hellbender.tools.spark.sv.evidence.KmerAndInterval (implements java.util.Map.Entry<K,V>)
  • org.broadinstitute.hellbender.tools.spark.sv.evidence.SVReadFilter (implements java.io.Serializable)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal