Package net.maizegenetics.pangenome.hapcollapse

Class Summary
Class	Description
MergeGVCFUtils	Created by zrm22 on 11/7/17.
FillIndelsIntoConsensus	This class is created to fill in the agreeing indels removed from the consensus haplotypes during the merge process.
PurgeSequencesFromAlignments	Created by edbuckler on 6/19/17.
RunGVCFTyper	Simple class to run the GVCFTyperPlugin until it gets integrated into TASSEL proper.
RunMergeAndCluster	This class takes a reference range, run through all the taxon with their variants List, create genotype table based on variant_id from PHG variants table.
VariantInfoConsensus
RunHapConsensusPipelinePlugin	This plugin creates consensus haplotypes.
CreateHaplotypesFromFasta	Created by edbuckler on 6/19/17.
QualityReportAnchorsToHaplotypes	Created by mm2842 on 6/20/17.
CompareAssembliesToReference	Simple little utility to compare assembly alignments to the reference genome
RefAltData	This class used when processing consensus data.
MergeGVCFPlugin	Created by zrm22 on 11/6/17.
ConsensusProcessingUtils	This class holds methods for processing consensus using the variants and alleles tables or data derived from them.
GVCFUtils	Created by zrm22 on 9/6/17.
FindHaplotypeClustersPlugin	Processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed in future steps into a consensus haplotype.
RunHapCollapsePipelinePlugin	Simple plugin to run the full Haplotype Collapse plugin.
GVCFTyperPlugin	Created by zrm22 on 8/1/17.