Uses of Class
net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE

Packages that use FillIndelsIntoConsensus.INDEL_MERGE_RULE

Package	Description
net.maizegenetics.pangenome.hapcollapse

Uses of FillIndelsIntoConsensus.INDEL_MERGE_RULE in net.maizegenetics.pangenome.hapcollapse

Methods in net.maizegenetics.pangenome.hapcollapse that return FillIndelsIntoConsensus.INDEL_MERGE_RULE

Modifier and Type	Method and Description
FillIndelsIntoConsensus.INDEL_MERGE_RULE	RunHapCollapsePipelinePlugin.mergeRule() The rule in which to resolve the conflicting Indels after consensus has been found.
static FillIndelsIntoConsensus.INDEL_MERGE_RULE	FillIndelsIntoConsensus.INDEL_MERGE_RULE.valueOf(String name) Returns the enum constant of this type with the specified name.
static FillIndelsIntoConsensus.INDEL_MERGE_RULE[]	FillIndelsIntoConsensus.INDEL_MERGE_RULE.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in net.maizegenetics.pangenome.hapcollapse with parameters of type FillIndelsIntoConsensus.INDEL_MERGE_RULE

Modifier and Type	Method and Description
static List<List<htsjdk.variant.variantcontext.VariantContext>>	FillIndelsIntoConsensus.addInIndels(ReferenceRange range, net.maizegenetics.dna.map.GenomeSequence refSequence, List<List<htsjdk.variant.variantcontext.VariantContext>> consensusSequences, List<List<htsjdk.variant.variantcontext.VariantContext>> rawConsensusWithIndels, int minComparableIndels, FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule) Method to add in the indels which were removed for the merging process.
RunHapCollapsePipelinePlugin	RunHapCollapsePipelinePlugin.mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE value) Set Indel Merge Rule.