Package net.maizegenetics.pangenome.hapcollapse
See: Description
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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. -
Enum Summary Enum Description INDEL_MERGE_RULE CLUSTERING_MODE CLUSTER_METHOD EMIT_MODE