Hierarchy For Package net.maizegenetics.pangenome.hapcollapse

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • net.maizegenetics.plugindef.AbstractPlugin (implements net.maizegenetics.plugindef.Plugin)
    • net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
    • net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
    • net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
    • net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
  • net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
  • net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
  • net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus
  • net.maizegenetics.pangenome.hapcollapse.GVCFUtils
  • net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
  • net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
  • net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
  • net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD
    • net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE
    • net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE