net.maizegenetics.pangenome.hapcollapse

Classes

• CompareAssembliesToReference
• CreateHaplotypesFromFasta
• FillIndelsIntoConsensus
• FindHaplotypeClustersPlugin
• GVCFTyperPlugin
• GVCFUtils
• MergeGVCFPlugin
• MergeGVCFUtils
• PurgeSequencesFromAlignments
• QualityReportAnchorsToHaplotypes
• RunGVCFTyper
• RunHapCollapsePipelinePlugin

Enums

• FillIndelsIntoConsensus.INDEL_MERGE_RULE
• FindHaplotypeClustersPlugin.CLUSTER_METHOD
• GVCFTyperPlugin.EMIT_MODE