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

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.broadinstitute.hellbender.tools.spark.sv.utils.CNVInputReader
  • 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.utils.ExtractOriginalAlignmentRecordsByNameSpark
  • org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants
  • org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFHeaderLines
  • org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervals
  • org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree<V> (implements java.lang.Iterable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeIterator (implements java.util.Iterator<E>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.PairedStrandedIntervalTreeOverlapperIterator (implements java.util.Iterator<E>)
  • org.apache.spark.Partitioner (implements scala.Serializable)
    • org.broadinstitute.hellbender.tools.spark.sv.utils.ComplexityPartitioner
  • com.esotericsoftware.kryo.Serializer<T>
    • org.broadinstitute.hellbender.tools.spark.sv.utils.KmerAndCount.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.PairedStrandedIntervalTree.Serializer<T>
    • org.broadinstitute.hellbender.tools.spark.sv.utils.Strand.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.Serializer<T>
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerLong.Serializer
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort.Serializer
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner<T,U> (implements java.lang.AutoCloseable)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.StrandedInterval
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SvCigarUtils
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead (implements org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.Mapping (implements htsjdk.samtools.util.Locatable)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVFileUtils
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVInterval (implements java.lang.Comparable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree<V> (implements java.lang.Iterable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.FwdIterator
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.OverlapIterator
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.RevIterator
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.ValuesIterator<V1> (implements java.util.Iterator<E>)
  • 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.utils.KmerAndCount (implements java.util.Map.Entry<K,V>)
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerShort (implements java.lang.Comparable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer (implements java.util.Iterator<E>)
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVDUSTFilteredKmerizer
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmerizer.ASCIICharSequence (implements java.lang.CharSequence)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVLocation (implements java.lang.Comparable<T>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVReferenceUtils
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils.IteratorFilter<T> (implements java.util.Iterator<E>)
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFReader
  • org.broadinstitute.hellbender.tools.spark.sv.utils.SVVCFWriter
  • org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec
  • org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MDElement
    • org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.DeletionMDElement
    • org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MatchMDElement
    • org.broadinstitute.hellbender.tools.spark.sv.utils.TextMDCodec.MismatchMDElement
  • htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, java.io.Serializable)
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVContext

Interface Hierarchy

• org.broadinstitute.hellbender.tools.spark.sv.utils.SingleSequenceReferenceAligner.TriFunction<T,U,V,W>
• org.broadinstitute.hellbender.tools.spark.sv.utils.SVIntervalTree.Entry<V1>

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.broadinstitute.hellbender.tools.spark.sv.utils.Strand
    • org.broadinstitute.hellbender.tools.spark.sv.utils.SVKmer.Base