A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W
I
- id() - function in net.maizegenetics.pangenome.api.AlleleInfo
- id() - function in net.maizegenetics.pangenome.api.HaplotypeNode
- id() - function in net.maizegenetics.pangenome.api.ReferenceRange
- Identifier for a unique reference range
- id() - function in net.maizegenetics.pangenome.api.Variant
- ImportHaplotypePathFilePlugin - class in net.maizegenetics.pangenome.hapCalling
- Plugin to import the haplotypePath files produced by ExportHaplotypePathToFilePlugin.
- includeSequences() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
- Whether to include sequences in haplotype nodes.
- includeSequences(Boolean) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
- Set Include Sequences.
- includeVariantContexts() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
- Whether to include variant contexts in haplotype nodes.
- includeVariantContexts(Boolean) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
- Set Include Variant Contexts.
- inclusionCountMap(Map) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
- inclusionFilename() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilename(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
- Set Inclusion File.
- inclusionFilenameDir() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
- The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
- Set Inclusion File Dir.
- inclusionFilenameDir() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
- The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir(String) - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
- Set Inclusion File Dir.
- inclusionOnly - enum entry in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD
- IndexHaplotypeKmersPlugin - class in net.maizegenetics.pangenome.hapCalling
- author edbuckler
- input() - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
- Input VCF file
- input(String) - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
- Set Input.
- inputFile() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
- GVCF File to be filtered.
- inputFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
- Set Input G V C F File.
- inputFileDirectory() - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
- Input file directory
- inputFileDirectory(String) - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
- Set Input File Directory.
- inputGVCFDir() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Input gvcf directory.
- inputGVCFDir(String) - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Set Input GVCF Directory.
- inputIntervalFile() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Input interval file to run GVCFTyper with.
- inputIntervalFile(String) - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
- Set Input Interval File.
- instance(String,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
- Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(GenomeSequence,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
- Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(GenomeSequence,String,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
- Instance method to allow for reference filling in missing for a file
- instance(GenomeSequence,List,boolean,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
- Instance method to build the GenomeSequence in memory using a List of VariantContexts
- instance(String,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(GenomeSequence,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(GenomeSequence,String,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- Instance method to add in missing as Ref from a file
- instance(GenomeSequence,List,boolean,String) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- Instance method to create a GenomeSequenc from a List of VariantContexts
- instance(GenomeSequence,List,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- instance(GenomeSequence,List,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
- INTER_ANCHOR - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType
- interGeneLength() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Number of base pairs to include for each intergenic region
- interGeneLength(Integer) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Set Length Of Inter Genes.
- interHapDivergence() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Percent each haplotype sequence should diverge from reference
- interHapDivergence(Integer) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
- Set Inter-Haplotype Divergence.
- intervalCoordinates() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
- intervalFile() - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
- Intervals file
- intervalFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
- Set Intervals.
- intervalFile() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
- Interval File used to create the VCF file
- intervalFile(String) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
- Set Interval File.
- intervalsFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
- Anchor Intervals file to be used when intervals are different than DB, e.g.
- intervalsFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
- Set Anchor Intervals File.
- intervalString() - function in net.maizegenetics.pangenome.api.ReferenceRange
- is_reference() - function in net.maizegenetics.pangenome.db_loading.GenoHaploData
- isAltSeqSameAsRefExcludingNs(String,String) - function in net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
- isFileGroupNew(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGData
- Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
- isFileGroupNew(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
- Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
- isFileGroupNew(String,String,String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
- Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
- isGca() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
- GCA fastas have long text as idLines.
- isGca(Boolean) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
- Set Is GCA.
- isIndel() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
- isIndel() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData
- isInitialized() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder
- isInitialized() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder
- isInitialized() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder
- isInitialized() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder
- isInitialized() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder
- isInitialized() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
- isInitialized() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
- isInteractive() - function in net.maizegenetics.plugindef.AbstractPlugin
- isPartOf(String) - function in net.maizegenetics.pangenome.api.ReferenceRange
- Returns whether this reference range is part of specifed group.
- isPhasedAcrossChromosomes() - function in net.maizegenetics.pangenome.db_loading.GenoHaploData
- isPhasedAcrossGenes() - function in net.maizegenetics.pangenome.db_loading.GenoHaploData
- isPlugin(String) - function in net.maizegenetics.plugindef.Plugin
- isPluginParameter(String) - function in net.maizegenetics.plugindef.AbstractPlugin
- isRefBlock(VariantContext) - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
- Simple method to check to see if the Variant is a reference block
- isRefBlock(VariantContext) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
- Simple method to determine if the current variant context is a reference block or not.
- isReference() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData
- isReferenceRecord(VariantContext) - function in net.maizegenetics.pangenome.hapcollapse.GVCFUtils
- Takes a VariantContext record and determines if the data is for a reference range block ro a variant.
- isSymbolic() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
- isTestMethod() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- Indication if the data is to be loaded against a test method.
- isTestMethod(Boolean) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
- Set Is Test Method.
- isVariant() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo