G-index

A B C D E F G H I K L M N O P Q R S T U V W

G

gbsDepth() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin: Depth for GBS
gbsDepth(Double) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin: Set GBS Depth.
geneEnd() - function in net.maizegenetics.pangenome.trimAnchors.AnchorInfo
geneFile() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Tab delimited .
geneFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Set Gene File.
GeneGFFData - class in net.maizegenetics.pangenome.db_loading
geneLength() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin: Number of base pairs to include for each gene region
geneLength(Integer) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin: Set Length Of Genes.
GenerateHaplotypeCallerScripts - class in net.maizegenetics.pangenome
GenerateRForPHG - class in net.maizegenetics.pangenome.pipelineTests: This class holds methods and classes to generate R code for PHG classes.
geneStart() - function in net.maizegenetics.pangenome.trimAnchors.AnchorInfo
GenoHaploData - class in net.maizegenetics.pangenome.db_loading: Object to hold data needed to populate the genotypes and haplotypes tables.
genomeFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Input assembly genome file from which to pull sequence
genomeFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Set Assembly Genome.
genomeFileID() - function in net.maizegenetics.pangenome.api.HaplotypeNode
genomeSequence(long,long) - function in net.maizegenetics.dna.map.GenomeSequence
genomeSequence(long,long) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genomeSequence(long,long) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeSequenceAsString(long,long) - function in net.maizegenetics.dna.map.GenomeSequence
genomeSequenceAsString(long,long) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genomeSequenceAsString(long,long) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeSize() - function in net.maizegenetics.dna.map.GenomeSequence
genomeSize() - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeSize() - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotype(Chromosome,int) - function in net.maizegenetics.dna.map.GenomeSequence
genotype(Chromosome,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotype(Chromosome,Position) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotype(Chromosome,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotype(Chromosome,Position) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeAsString(Chromosome,int) - function in net.maizegenetics.dna.map.GenomeSequence
genotypeAsString(Chromosome,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome,int,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome,Position) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeAsString(Chromosome,int,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeAsString(Chromosome,Position) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeString() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getAdjustedMummerCoordEntry(String,int,boolean) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
getAllFields() - function in com.google.protobuf.GeneratedMessageV3
getAllFields() - function in com.google.protobuf.GeneratedMessageV3.Builder
getAllFields() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getAllFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getAllFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getAllFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getAllFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getAllFields() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getAllTaxaGroupNames() - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns a list of all taxa group names from the taxa_groups table
getAllTaxaGroupNames() - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns a list of all taxa group names from the taxa_groups table
getAllTaxaGroupNames() - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns a list of all taxa group names from the taxa_groups table
getAltDepth() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
getAnchorFromIntervalsFile(String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getAnchorRangeSet(Map) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Create a RangeSet from a map of ranges
getAnchorRangeSet(RangeMap) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getAsmContig() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: string asmContig = 6;
getAsmContig() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmContig = 6;
getAsmContig() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: string asmContig = 6;
getAsmContigBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: string asmContig = 6;
getAsmContigBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmContig = 6;
getAsmContigBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: string asmContig = 6;
getAsmEndCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: int32 asmEndCoordinate = 8;
getAsmEndCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 asmEndCoordinate = 8;
getAsmEndCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: int32 asmEndCoordinate = 8;
getAsmEndPos() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getAsmStartCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: int32 asmStartCoordinate = 7;
getAsmStartCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 asmStartCoordinate = 7;
getAsmStartCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: int32 asmStartCoordinate = 7;
getAsmStartPos() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getAsmStrand() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: string asmStrand = 9;
getAsmStrand() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmStrand = 9;
getAsmStrand() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: string asmStrand = 9;
getAsmStrandBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: string asmStrand = 9;
getAsmStrandBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmStrand = 9;
getAsmStrandBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: string asmStrand = 9;
getButtonName() - function in net.maizegenetics.pangenome.api.FilterGraphPlugin
getButtonName() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getButtonName() - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin
getButtonName() - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getButtonName() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getButtonName() - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin
getButtonName() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getButtonName() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getButtonName() - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getButtonName() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getButtonName() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
getButtonName() - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getButtonName() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getButtonName() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getButtonName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getButtonName() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
getChecksumForFile(File,String) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
getChecksumForString(String,String) - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
getChrom() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
getChromNamesForHaplotype(String,int,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method grabs a list of distinct chromosome names for a genome_interval version
getChromNamesForHaplotype(String,int,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method grabs a list of distinct chromosome names for a genome_interval version
getChromNamesForHaplotype(String,int,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method grabs a list of distinct chromosome names for a genome_interval version
getChromosome() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: string chromosome = 3;
getChromosome() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string chromosome = 3;
getChromosome() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: string chromosome = 3;
getChromosomeBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: string chromosome = 3;
getChromosomeBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string chromosome = 3;
getChromosomeBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: string chromosome = 3;
getCitation() - function in net.maizegenetics.plugindef.AbstractPlugin
getConsensusDataMap() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
getCoordsEntriesForAnchor(Range,RangeMap) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getCoordsRangeMap(List,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Create range map from list of entries from a Mummer coordinates file
getDataFromAssembly(String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
GetDBConnectionPlugin - class in net.maizegenetics.pangenome.db_loading: Plugin takes a configFile with db specifics and a boolean indicating whether a new db shoudl be created.
getDbTaxaNames() - function in net.maizegenetics.pangenome.db_loading.PHGData: Gets a list of the taxa currently in the database.
getDbTaxaNames() - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Gets a list of the taxa currently in the database.
getDbTaxaNames() - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Gets a list of the taxa currently in the database.
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
getDefaultInstance() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getDefaultInstanceForType() - function in com.google.protobuf.MessageLiteOrBuilder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
getDefaultInstanceForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
getDescriptor() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
getDescriptorForType() - function in com.google.protobuf.GeneratedMessageV3
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getDescriptorForType() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
getDescriptorForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
getEdgeProbability() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto: double edgeProbability = 3;
getEdgeProbability() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: double edgeProbability = 3;
getEdgeProbability() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProtoOrBuilder: double edgeProbability = 3;
getEnd() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: int32 end = 5;
getEnd() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 end = 5;
getEnd() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: int32 end = 5;
getEntryFromTabDelimitedLine(String,int,int) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Returns the value for a specific column in a tab-delimited string
GetFastaSequenceLengths - class in net.maizegenetics.pangenome: Created by terry on 3/19/17.
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getFieldBuilder(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
getGameteGroupIDFromTaxaList(List) - function in net.maizegenetics.pangenome.db_loading.PHGData: Takes a list of taxa and returns the corresponding gamete_group_id or 0
getGameteGroupIDFromTaxaList(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Takes a list of taxa and returns the corresponding gamete_group_id or 0
getGameteGroupIDFromTaxaList(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Takes a list of taxa and returns the corresponding gamete_group_id or 0
getGenoidFromLine(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Return genoid
getGenoidFromLine(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Return genoid
getGenoidFromLine(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Return genoid
getGenoidsForTaxa(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
getGenomeFileHashFromGenoidandFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table.
getGenomeFileHashFromGenoidandFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table.
getGenomeFileHashFromGenoidandFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table.
getGenomeFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: int32 genomeFileId = 4;
getGenomeFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 genomeFileId = 4;
getGenomeFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: int32 genomeFileId = 4;
getGenomeFileIdFromGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Gets the id from the genome_file_data table based on the genoid .
getGenomeFileIdFromGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Gets the id from the genome_file_data table based on the genoid .
getGenomeFileIdFromGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Gets the id from the genome_file_data table based on the genoid .
getGenomeFileIdFromGenoidAndFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Gets the id from the genome_file_data table based on the genoid and a filename
getGenomeFileIdFromGenoidAndFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Gets the id from the genome_file_data table based on the genoid and a filename
getGenomeFileIdFromGenoidAndFile(int,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Gets the id from the genome_file_data table based on the genoid and a filename
getGenomeSequenceValues() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
getGvcfFile() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto: string gvcfFile = 2;
getGvcfFile() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder: string gvcfFile = 2;
getGvcfFile() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProtoOrBuilder: string gvcfFile = 2;
getGvcfFileBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto: string gvcfFile = 2;
getGvcfFileBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder: string gvcfFile = 2;
getGvcfFileBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProtoOrBuilder: string gvcfFile = 2;
getGvcfFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: int32 gvcfFileId = 5;
getGvcfFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 gvcfFileId = 5;
getGvcfFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: int32 gvcfFileId = 5;
getGvcfIdToFile(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFile(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFile(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfIdToFileOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
getGvcfRemoteToLocalFiles() - function in net.maizegenetics.pangenome.api.VariantUtils: This method returns the gvcfRemoteToLocalFiles map
getHapCountsIDAndDataForVersionMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
getHapCountsIDAndDataForVersionMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
getHapCountsIDAndDataForVersionMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
getHapCountsIDAndPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
getHapCountsIDAndPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
getHapCountsIDAndPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
getHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: int32 hapId = 1;
getHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 hapId = 1;
getHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: int32 hapId = 1;
getHapidForGenoidHapNumber(int,int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns hapid for given line name and hap_number
getHapidForGenoidHapNumber(int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns hapid for given line name and hap_number
getHapidForGenoidHapNumber(int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns hapid for given line name and hap_number
getHapidHapNumberLineNamesForLines(List) - function in net.maizegenetics.pangenome.db_loading.PHGData: Retrieves line name and hapnumber, and returns them with the hapid.
getHapidHapNumberLineNamesForLines(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Retrieves line name and hapnumber, and returns them with the hapid.
getHapidHapNumberLineNamesForLines(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Retrieves line name and hapnumber, and returns them with the hapid.
getHapidMapFromLinenameHapNumber() - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns a map of created from the genotypes and haplotypes table.
getHapidMapFromLinenameHapNumber() - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns a map of created from the genotypes and haplotypes table.
getHapidMapFromLinenameHapNumber() - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns a map of created from the genotypes and haplotypes table.
getHapidsForGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns list of hapids for a given line name
getHapidsForGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns list of hapids for a given line name
getHapidsForGenoid(int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns list of hapids for a given line name
getHaplotypeEdges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeEdgesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
getHaplotypeIDFromFastaIDLine(String,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
getHaplotypeIDFromFastaIDLine(String,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
getHaplotypeIDFromFastaIDLine(String,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
getHaplotypeList(int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
getHaplotypeList(int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
getHaplotypeList(int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
getHaplotypeListIDfromHash(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
getHaplotypeListIDfromHash(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
getHaplotypeListIDfromHash(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
getHaplotypeNodes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeNodesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
getHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequenceBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequenceOrBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequenceOrBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHaplotypeSequenceOrBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
getHostIpAddr() - function in net.maizegenetics.pangenome.smallseq.CreateTestGenomes
getIcon() - function in net.maizegenetics.pangenome.api.FilterGraphPlugin
getIcon() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getIcon() - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin
getIcon() - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getIcon() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getIcon() - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin
getIcon() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getIcon() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getIcon() - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getIcon() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getIcon() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getIcon() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getIcon() - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getIcon() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getIcon() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
getIcon() - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getIcon() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getIcon() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getIcon() - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getIcon() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto: int32 id = 1;
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder: int32 id = 1;
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProtoOrBuilder: int32 id = 1;
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: int32 id = 1;
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 id = 1;
getId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: int32 id = 1;
getIndelRanges(RangeMap) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
getInitializationErrorString() - function in com.google.protobuf.AbstractMessage
getInitializationErrorString() - function in com.google.protobuf.AbstractMessage.Builder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getInitializationErrorString() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getInputs() - function in net.maizegenetics.plugindef.AbstractPlugin
getInstance(Array,ReferenceRange,double,String,int) - function in net.maizegenetics.pangenome.api.HaplotypeSequence: Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of the original mutable object Haplotype sequences are always gzip compressed, stored as byte array.
getInstance(String,ReferenceRange,double,String) - function in net.maizegenetics.pangenome.api.HaplotypeSequence: Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of the original mutable object
getInstanceFromHapidCountMap(TreeMap,Map,double) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getInstanceFromHapidCounts(TreeMap,Multiset,double) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getInstanceFromNodeCounts(TreeMap,Multiset,double) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getIntervalRangesWithIDForChrom(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns sorted treeRangeMap of Positions for specified chromosome
getIntervalRangesWithIDForChrom(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns sorted treeRangeMap of Positions for specified chromosome
getIntervalRangesWithIDForChrom(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns sorted treeRangeMap of Positions for specified chromosome
getLeftHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto: int32 leftHapId = 1;
getLeftHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: int32 leftHapId = 1;
getLeftHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProtoOrBuilder: int32 leftHapId = 1;
getLen() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
getLength() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto: int32 length = 1;
getLength() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: int32 length = 1;
getLength() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProtoOrBuilder: int32 length = 1;
getLineNameHapNumberFromHapid(int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method to retrieve both a line name and the hap number given a hapid.
getLineNameHapNumberFromHapid(int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method to retrieve both a line name and the hap number given a hapid.
getLineNameHapNumberFromHapid(int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method to retrieve both a line name and the hap number given a hapid.
getListeners() - function in net.maizegenetics.plugindef.AbstractPlugin
getLnProbObsGivenState(int,int) - function in net.maizegenetics.analysis.imputation.EmissionProbability
getLnTransitionProbability(int,int) - function in net.maizegenetics.analysis.imputation.TransitionProbability
getLongFromRefAltData(RefAltData) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils: RefAltData comes from processing the Longs stored for each haplotype.
getLongFromVMData(int,VariantMappingData) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Takes an ID and a VariantMappingData object and creates a list of variant_ids with additional data.
getLongListOfVariantData(List,Map) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Takes a list of variantIdhash to VariantMappingData and creates a list of "long" values, that represents the variant context for each entry
getLongRefRecord(int,int,int) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Takes a reference length, depth and start position on the chromosome.
getLongVariantRecord(int,int,int,byte,int) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Takes a variantMapping id, reference depth, alternate depth, indication as to if is an indel, and a dummy int Returns a long formatted with this data.
getMapFromFasta(String) - function in net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence: Load a fasta file in a map, headers are keys and sequences are values assumes a fasta file in which sequences are not breaked between lines
getMapFromFasta(String) - function in net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
getMeanDepth(String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to compute the mean of the depths.
getMeanDepth(String,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getMedianDepth(String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to calculate the Median depth for a GVCF file.
getMedianDepth(String,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getMenu() - function in net.maizegenetics.plugindef.AbstractPlugin
getMethodDescriptionFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method queries the db methods table for the description field given a methods name
getMethodDescriptionFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method queries the db methods table for the description field given a methods name
getMethodDescriptionFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method queries the db methods table for the description field given a methods name
getMethodIdFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns method_id given a method name.
getMethodIdFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns method_id given a method name.
getMethodIdFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns method_id given a method name.
getMethods(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: repeated string methods = 6;
getMethods(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: repeated string methods = 6;
getMethods(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: repeated string methods = 6;
getMethodsBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: repeated string methods = 6;
getMethodsBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: repeated string methods = 6;
getMethodsBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: repeated string methods = 6;
getMethodsCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: repeated string methods = 6;
getMethodsCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: repeated string methods = 6;
getMethodsCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: repeated string methods = 6;
getMethodsList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: repeated string methods = 6;
getMethodsList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: repeated string methods = 6;
getMethodsList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: repeated string methods = 6;
getModeDepth(String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to get the mode of the depth.
getModeDepth(String,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getMyAltAllele() - function in net.maizegenetics.pangenome.api.DBVariant
getMyAncestralID() - function in net.maizegenetics.pangenome.api.DBVariant
getMyChromosome() - function in net.maizegenetics.pangenome.api.DBVariant
getMyRefAllele() - function in net.maizegenetics.pangenome.api.DBVariant
getMyStartPosition() - function in net.maizegenetics.pangenome.api.DBVariant
getMyVariantID() - function in net.maizegenetics.pangenome.api.DBVariant
getNumAlignedBases(RangeSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getNumberOfStates() - function in net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.GeneratedMessageV3
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getOneofFieldDescriptor(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getPairedSimilarFragmentsFromMummer(List) - function in net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors: Grab the ref and asm start/end positions, determine asm strand direction, calculate a score, and store all to a list of PairedSimilarFragments The score is calculated as: (%id * asmLen)/100 casted to int
getPanel() - function in net.maizegenetics.plugindef.AbstractPlugin
getParameter(Enum) - function in net.maizegenetics.plugindef.AbstractPlugin
getParentFrame() - function in net.maizegenetics.plugindef.AbstractPlugin
getParserForType() - function in com.google.protobuf.Message
getParserForType() - function in com.google.protobuf.MessageLite
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
getParserForType() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
getPathIdsForReadMappingIds(List) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
getPathIdsForReadMappingIds(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
getPathIdsForReadMappingIds(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
getPathsForTaxonMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair.
getPathsForTaxonMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair.
getPathsForTaxonMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair.
getPluginInstance(String,Frame) - function in net.maizegenetics.plugindef.Plugin
getPosition() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
getProbObsGivenState(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getProbObsGivenState(int,int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getQualityScore() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto: double qualityScore = 3;
getQualityScore() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: double qualityScore = 3;
getQualityScore() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProtoOrBuilder: double qualityScore = 3;
getRangesForChrom(Map,Chromosome,DBLoadingUtils.AnchorType) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getRangesForChrom(Map,Chromosome,DBLoadingUtils.AnchorType) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getReadMappingId(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id.
getReadMappingId(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id.
getReadMappingId(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id.
getReadMappingIdsForTaxaMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGData: This method takes a list of taxa and a method name.
getReadMappingIdsForTaxaMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: This method takes a list of taxa and a method name.
getReadMappingIdsForTaxaMethod(List,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: This method takes a list of taxa and a method name.
getReadMappingsForId(int) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method to get the Read Mapping data from the DB using the read_mapping_id.
getReadMappingsForId(int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method to get the Read Mapping data from the DB using the read_mapping_id.
getReadMappingsForId(int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method to get the Read Mapping data from the DB using the read_mapping_id.
getReadMappingsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method to get the mapping ids by method
getReadMappingsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method to get the mapping ids by method
getReadMappingsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method to get the mapping ids by method
getRefDepth() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
getRefEndPos() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getReferenceName() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: string referenceName = 2;
getReferenceName() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string referenceName = 2;
getReferenceName() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: string referenceName = 2;
getReferenceNameBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: string referenceName = 2;
getReferenceNameBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string referenceName = 2;
getReferenceNameBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: string referenceName = 2;
getReferenceRange() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
getReferenceRangeID() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto: int32 referenceRangeID = 2;
getReferenceRangeID() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: int32 referenceRangeID = 2;
getReferenceRangeID() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProtoOrBuilder: int32 referenceRangeID = 2;
getReferenceRanges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRanges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRanges(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getReferenceRangesOrBuilderList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProtoOrBuilder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
getRefLineName(Connection) - function in net.maizegenetics.pangenome.api.CreateGraphUtils: Returns the line name of the reference genotype
getRefRangeIDFromString(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns reference range id
getRefRangeIDFromString(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns reference range id
getRefRangeIDFromString(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns reference range id
getRefRangesForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method to return all reference ranges associated with a specified method name
getRefRangesForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method to return all reference ranges associated with a specified method name
getRefRangesForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method to return all reference ranges associated with a specified method name
getRefStartPos() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getRegionCoverage(RangeSet,Range) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: This method takes a RangeSet of integers, and a single range.
getRegionCoverage(RangeSet,Range) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.GeneratedMessageV3
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.GeneratedMessageV3.Builder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getRepeatedField(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getRepeatedFieldBuilder(Descriptors.FieldDescriptor,int) - function in com.google.protobuf.GeneratedMessageV3.Builder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getRepeatedFieldCount(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getRightHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto: int32 rightHapId = 2;
getRightHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: int32 rightHapId = 2;
getRightHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProtoOrBuilder: int32 rightHapId = 2;
getScore() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getSeqHash() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto: string seqHash = 4;
getSeqHash() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: string seqHash = 4;
getSeqHash() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProtoOrBuilder: string seqHash = 4;
getSeqHashBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto: string seqHash = 4;
getSeqHashBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: string seqHash = 4;
getSeqHashBytes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProtoOrBuilder: string seqHash = 4;
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
getSerializedSize() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
getStart() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto: int32 start = 4;
getStart() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 start = 4;
getStart() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProtoOrBuilder: int32 start = 4;
getStartEndCoordinates(String,boolean) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Find the start/end coordinates from a tab-delmimited Mummer4 coords file entry
getStrand() - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
getTaxa(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: repeated string taxa = 3;
getTaxa(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: repeated string taxa = 3;
getTaxa(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: repeated string taxa = 3;
getTaxaBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: repeated string taxa = 3;
getTaxaBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: repeated string taxa = 3;
getTaxaBytes(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: repeated string taxa = 3;
getTaxaCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: repeated string taxa = 3;
getTaxaCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: repeated string taxa = 3;
getTaxaCount() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: repeated string taxa = 3;
getTaxaForPathMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Method to get a list of all genoid line_names that have paths for method = method_name.
getTaxaForPathMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Method to get a list of all genoid line_names that have paths for method = method_name.
getTaxaForPathMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Method to get a list of all genoid line_names that have paths for method = method_name.
getTaxaForTaxaGroup(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Get the taxa that make up the specified taxa group
getTaxaForTaxaGroup(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Get the taxa that make up the specified taxa group
getTaxaForTaxaGroup(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Get the taxa that make up the specified taxa group
getTaxaGroupIDFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns taxa_grp_id given a taxa group name.
getTaxaGroupIDFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns taxa_grp_id given a taxa group name.
getTaxaGroupIDFromName(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns taxa_grp_id given a taxa group name.
getTaxaList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto: repeated string taxa = 3;
getTaxaList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: repeated string taxa = 3;
getTaxaList() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder: repeated string taxa = 3;
getTaxonPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGData: Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
getTaxonPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter: Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
getTaxonPathsForMethod(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess: Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
getToolTipText() - function in net.maizegenetics.pangenome.api.FilterGraphPlugin
getToolTipText() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getToolTipText() - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin
getToolTipText() - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getToolTipText() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getToolTipText() - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin
getToolTipText() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getToolTipText() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getToolTipText() - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getToolTipText() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
getToolTipText() - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getToolTipText() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getToolTipText() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getToolTipText() - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getToolTipText() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
getTransitionProbability(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
getUnknownFields() - function in com.google.protobuf.GeneratedMessageV3
getUnknownFields() - function in com.google.protobuf.GeneratedMessageV3.Builder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
getUnknownFields() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
getUsage() - function in net.maizegenetics.plugindef.AbstractPlugin
getUsageHTML() - function in net.maizegenetics.plugindef.AbstractPlugin
getValue() - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.GenomeFileType
getValue() - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType
getVariantContextFromHaplotypeNodeList(List) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils: Method to extract the VCF VariantContexts from a List of HaplotypeNodes
getVariantContextFromHaplotypePath(HaplotypePath) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils: Method to extract the VCF VariantContexts from the HaplotypePath.
getVariantData(String,Map,HaplotypeNode.VariantInfo,Connection) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Method will return a Tuple of the hash of (chrom, start_position, refAlleleID, altAlleleID) and a VariantMappingData record The alleleHashMap should contain the initial alleles pre-populated.
getVariantId() - function in net.maizegenetics.pangenome.hapcollapse.RefAltData
gffFile() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin: Tab delimited .
gffFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin: Set Gene File.
graphExportBasename() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The base name for R-igraph export files.
graphExportBasename(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Graph Export.
GraphIO - class in net.maizegenetics.pangenome.api
graphToHapsInRefRangeVectors(HaplotypeGraph,Array,boolean,boolean) - function in net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG: Given a PHG HaplotypeGraph, create a set of vectors representing data for all Haplotypes/Nodes in the graph.
graphToRefRangeVectors(HaplotypeGraph,Array) - function in net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG: Given a PHG HaplotypeGraph, create a set of vectors representing data for all ReferenceRanges in the graph.
GraphUtils - class in net.maizegenetics.pangenome.api
groupMethods() - function in net.maizegenetics.pangenome.api.ReferenceRange: Returns group methods that this range belongs.
gvcf() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
GVCF - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.GenomeFileType
gvcfFileID() - function in net.maizegenetics.pangenome.api.HaplotypeNode
gvcfFileId() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
gvcfFilePath(int) - function in net.maizegenetics.pangenome.api.VariantUtils: This method returns the gvcf file path for the given gvcfId.
GVCFGenotypeSequence - class in net.maizegenetics.pangenome.fastaExtraction: GVCFGenotypeSequence This class should be used instead of GVCFSequence when you want to have diploid calls being returned.
gVCFInputDir() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Directory holding the GVCF files to be filtered.
gVCFInputDir(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Gvcf Dir.
gVCFOutputDir() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Directory for gvcf files to be output for later use
gVCFOutputDir(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set GVCF Output Dir.
GVCFSequence - class in net.maizegenetics.pangenome.fastaExtraction: GVCFSequence.
GVCFStats - class in net.maizegenetics.pangenome
GVCFTyperPlugin - class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 8/1/17.
GVCFTyperPlugin.EMIT_MODE - class in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
GVCFUtils - class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 9/6/17.

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