Hierarchy For Package org.broadinstitute.hellbender.tools.copynumber

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • org.broadinstitute.hellbender.cmdline.CommandLineProgram (implements org.broadinstitute.barclay.argparser.CommandLinePluginProvider)
    • org.broadinstitute.hellbender.tools.copynumber.CallCopyRatioSegments
    • org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts
    • org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy
    • org.broadinstitute.hellbender.tools.copynumber.FilterIntervals
    • org.broadinstitute.hellbender.engine.GATKTool
      • org.broadinstitute.hellbender.tools.copynumber.AnnotateIntervals
      • org.broadinstitute.hellbender.tools.copynumber.PostprocessGermlineCNVCalls
      • org.broadinstitute.hellbender.tools.copynumber.PreprocessIntervals
      • org.broadinstitute.hellbender.engine.WalkerBase
        • org.broadinstitute.hellbender.engine.LocusWalker
          • org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts
        • org.broadinstitute.hellbender.engine.ReadWalker
          • org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts
    • org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller
    • org.broadinstitute.hellbender.tools.copynumber.ModelSegments
    • org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram (implements java.io.Serializable)
      • org.broadinstitute.hellbender.tools.copynumber.CreateReadCountPanelOfNormals
      • org.broadinstitute.hellbender.engine.spark.GATKSparkTool
        • org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark
          • org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark

Enum Class Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • org.broadinstitute.hellbender.tools.copynumber.CollectReadCounts.Format
    • org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.RunMode
    • org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.RunMode
    • org.broadinstitute.hellbender.tools.copynumber.ModelSegments.RunMode