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lastReferenceRange() - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns the last reference range in this graph.

lastReferenceRange(Chromosome) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns the last reference range for the given chromosome.

leftEdges(HaplotypeNode) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns List of Left HaplotypeEdges for given HaplotypeNode

leftHapNode() - function in net.maizegenetics.pangenome.api.HaplotypeEdge

HaplotypeNode to the left of the current edge.

leftTrimCount() - function in net.maizegenetics.pangenome.trimAnchors.AnchorInfo

 

length() - function in net.maizegenetics.pangenome.api.AlleleInfo

 

length() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo

 

length() - function in net.maizegenetics.pangenome.api.HaplotypeSequence

 

likelihood() - function in net.maizegenetics.pangenome.api.HaplotypePath

Likelihood of haplotype path calculated from all included haplotype nodes

line_data() - function in net.maizegenetics.pangenome.db_loading.GenoHaploData

 

line_name() - function in net.maizegenetics.pangenome.db_loading.GenoHaploData

 

lineName() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin

Name name to be stored in the genotypes table, e.g.

lineName(String) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin

Set Line Name.

listTaxa() - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.

loadAssemblyDataToDB(int,String,Connection,Map,String,int) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

Load the assembly haplotype data to the database

loadInitialAssemblyData(String,String,int,Connection,Map,List,boolean) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

load initial genotype and method data to the database

localGVCFFolder() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Local folder to which gvcf file will be downloaded.

localGVCFFolder(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Set local gvcf folder path

longestIncreasingSubsequenceLAGAN(List) - function in net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors

 

longestIndel - enum entry in net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE

 

longListToByteArray(Collection) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils

 

lowerPoissonBound() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin

Lower Poisson Bound used for filtering.

lowerPoissonBound(Double) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin

Set Lower Poisson Bound.

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