Hierarchy For Package org.broadinstitute.hellbender.tools.spark.pathseq

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.broadinstitute.hellbender.cmdline.CommandLineProgram (implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
    • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildKmers
    • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBuildReferenceTaxonomy
    • org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram (implements java.io.Serializable)
      • org.broadinstitute.hellbender.engine.spark.GATKSparkTool
        • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqBwaSpark
        • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqFilterSpark
        • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark
        • org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqScoreSpark
  • org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilterSpark (implements org.apache.spark.api.java.function.Function<T1,R>)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBuildReferenceTaxonomyUtils
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAligner
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaAlignerSpark (implements java.lang.AutoCloseable)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection (implements java.io.Serializable)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaFilter
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaUtils
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSFilter (implements java.lang.AutoCloseable)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSFilterArgumentCollection (implements java.io.Serializable)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerCollection
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerUtils
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSPairedUnpairedSplitterSpark
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenAlignmentHit
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenReferenceTaxonProperties
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSPathogenTaxonScore
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSScoreArgumentCollection (implements java.io.Serializable)
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSScorer
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyConstants
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSTree
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode
  • org.broadinstitute.hellbender.tools.spark.pathseq.PSUtils
  • org.broadinstitute.hellbender.engine.filters.ReadFilter (implements java.util.function.Predicate<T>, java.io.Serializable)
    • org.broadinstitute.hellbender.tools.spark.pathseq.ContainsKmerReadFilter
    • org.broadinstitute.hellbender.tools.spark.pathseq.HostAlignmentReadFilter
    • org.broadinstitute.hellbender.tools.spark.pathseq.MarkedOpticalDuplicateReadFilter (implements java.io.Serializable)
  • com.esotericsoftware.kryo.Serializer<T>
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerBloomFilter.Serializer
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSKmerSet.Serializer
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSTaxonomyDatabase.Serializer
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSTree.Serializer
    • org.broadinstitute.hellbender.tools.spark.pathseq.PSTreeNode.Serializer