Uses of Class
net.maizegenetics.pangenome.api.HaplotypePath

Packages that use HaplotypePath

Package	Description
net.maizegenetics.pangenome.api
net.maizegenetics.pangenome.hapCalling

Uses of HaplotypePath in net.maizegenetics.pangenome.api

Methods in net.maizegenetics.pangenome.api that return HaplotypePath

Modifier and Type	Method and Description
HaplotypePath	HaplotypeGraph.path(net.maizegenetics.taxa.Taxon taxon) Returns most probable HaplotypePath for each Chromosome given the specified Taxon.

Methods in net.maizegenetics.pangenome.api that return types with arguments of type HaplotypePath

Modifier and Type	Method and Description
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path() Returns most probable HaplotypePath for each Chromosome.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(List<HaplotypeNode> nodes) Returns most probable HaplotypePath for each Chromosome given the specified list of known HaplotypeNodes.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(String taxon) Returns most probable HaplotypePath for each Chromosome given the specified taxon.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(String taxon, List<HaplotypeNode> nodes) Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes.
TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath>	HaplotypeGraph.path(net.maizegenetics.taxa.Taxon taxon, List<HaplotypeNode> nodes) Returns most probable HaplotypePath for each Chromosome given the specified Taxon and list of known HaplotypeNodes.

Method parameters in net.maizegenetics.pangenome.api with type arguments of type HaplotypePath

Modifier and Type	Method and Description
static SortedSet<Integer>	GraphUtils.path(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths) Returns sorted set of haplotype ids from the given paths.
static SortedSet<HaplotypeNode>	GraphUtils.pathsToNodes(TreeMap<net.maizegenetics.dna.map.Chromosome,HaplotypePath> paths)

Uses of HaplotypePath in net.maizegenetics.pangenome.hapCalling

Methods in net.maizegenetics.pangenome.hapCalling with parameters of type HaplotypePath

Modifier and Type	Method and Description
static void	HapCallingUtils.callSNPsFromHaplotypePath(HaplotypeGraph graph, HaplotypePath bestPath, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
static List<htsjdk.variant.variantcontext.VariantContext>	HapCallingUtils.getVariantContextFromHaplotypePath(HaplotypePath bestPath) Method to extract the VCF VariantContexts from the HaplotypePath.