Package net.maizegenetics.pangenome.hapcollapse

Class Summary

Class	Description
CompareAssembliesToReference	Simple little utility to compare assembly alignments to the reference genome
CreateHaplotypesFromFasta	Created by edbuckler on 6/19/17.
FillIndelsIntoConsensus	This class is created to fill in the agreeing indels removed from the consensus haplotypes during the merge process.
FindHaplotypeClustersPlugin	Processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed in future steps into a consensus haplotype.
GVCFTyperPlugin	Created by zrm22 on 8/1/17.
GVCFUtils	Created by zrm22 on 9/6/17.
MergeGVCFPlugin	Created by zrm22 on 11/6/17.
MergeGVCFUtils	Created by zrm22 on 11/7/17.
PurgeSequencesFromAlignments	Created by edbuckler on 6/19/17.
QualityReportAnchorsToHaplotypes	Created by mm2842 on 6/20/17.
RunGVCFTyper	Simple class to run the GVCFTyperPlugin until it gets integrated into TASSEL proper.
RunHapCollapsePipelinePlugin	Simple plugin to run the full Haplotype Collapse plugin.

Enum Summary

Enum	Description
FillIndelsIntoConsensus.INDEL_MERGE_RULE
FindHaplotypeClustersPlugin.CLUSTER_METHOD
GVCFTyperPlugin.EMIT_MODE