E-index

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E

edge(HaplotypeNode,HaplotypeNode) - function in net.maizegenetics.pangenome.api.HaplotypeGraph: Returns optional edge between given nodes.
EDGE - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType
edgeProbability() - function in net.maizegenetics.pangenome.api.HaplotypeEdge: Probability that the node to the right of this edge rightHapNode is the next HaplotypeNode when traversing the graph from left to right.
edges() - function in net.maizegenetics.pangenome.api.HaplotypePath: Haplotype Edges that create this HaplotypePath
emissionMethod() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Emission Method
emissionMethod(ReferenceRangeEmissionProbability.METHOD) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Emission Method.
emitModeParam() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Emit Mode for running GVCFTyper.
emitModeParam(GVCFTyperPlugin.EMIT_MODE) - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Emit_mode.
encodeHapCountsArrayFromFile(String) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeHapCountsArrayFromMultiset(Multiset,Multiset) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils: THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts.
encodeHapidListToByteArray(List) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodePathArrayForMultipleLists(List) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodePathArrayFromSet(Set) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodePathsFromIntArray(List) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils: This method takes a list of haplotype ids and compresses them to a byte array.
encodeRefBlockToLong(int,int,int) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils: Encode a reference block to a Long
encodeSelectedVCFRegionsToByteArray(String,boolean,boolean,Range) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVariantContextListToByteArray(List,boolean) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVariantContextStreamToByteArray(Stream,boolean,boolean) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVariantLongListToByteArray(List) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Method takes a List of Long objects and converts to a Snappy compressed byte stream
encodeVariantToLong(int,int,int,boolean) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils: Encode variant information as a Long
encodeVCFFileToByteArray(String,boolean,boolean) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils
end() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
end() - function in net.maizegenetics.pangenome.api.ReferenceRange: End position of reference range, inclusive
end() - function in net.maizegenetics.pangenome.db_loading.GeneGFFData
endNodes() - function in net.maizegenetics.pangenome.api.HaplotypeGraph: Returns list of HaplotypeNodes that end graph.
endNodes(Chromosome) - function in net.maizegenetics.pangenome.api.HaplotypeGraph
entryPoint() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Where to begin processing.
entryPoint(AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Assembly Entry Point.
equals(Object) - function in net.maizegenetics.pangenome.api.ReferenceRange
equals(Object) - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
equals(Object) - function in net.maizegenetics.pangenome.db_loading.VariantMappingData
equals(Object) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.VariantInfoConsensus
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto
equals(Object) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto
EvaluateHaplotypeFastaInKnownIBDRegions - class in net.maizegenetics.pangenome.pipelineTests: Unit test to evaluate fasta file generated from GVCF files for anchors in IBD regions to B73 Get all the anchorIDs in the IBD region of chromosome 10 Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (alternative).
exclusionCountMap(Map) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
exportHaplotypeFile() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Text file to store haplotype scoring
exportHaplotypeFile(String) - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Export Haplo File.
ExportHaplotypePathToFilePlugin - class in net.maizegenetics.pangenome.hapCalling: Plugin to export the Multimapexported by a Path finding algorithm to a directory of text files Created by zrm22 on 10/13/17.
exportMergedRegions(Map,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Utility method to export out the merged regions
exportPHGToFlapjack(HaplotypeGraph,String) - function in net.maizegenetics.pangenome.api.RMethods
ExportVCForTaxonMethodPlugin - class in net.maizegenetics.pangenome.hapCalling: Exports variant context lists to vcf file.
extendedBedFile() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Name for the extended bed file
extendedBedFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Set Extended Bed File.
extractAnchorVariantContextsFromAssemblyAlignments(GenomeSequence,String,RangeSet,Map,RangeMap) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method to build the list of VariantContexts based on the mapped coordinates and the SNPs
extractFasta(String,String,String) - function in net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU: Method to setup the run by creating a file list
ExtractFastaFromGVCFCBSU - class in net.maizegenetics.pangenome.fastaExtraction: Command line program to pull the sequence for each taxa where each row is an anchor Multithreads the extraction so it can run quickly TODO Create a plugin which will do this once we recode GVCF->Fasta Created by zrm22 on 5/2/17.
extractFastaSequence(List,ReferenceRange) - function in net.maizegenetics.pangenome.fastaExtraction.ExtractFastaUtils: Method to extract out a fasta sequence given a list of variantContexts This will fill in Ns whenever we do not have a variant context record for a given position
ExtractFastaUtils - class in net.maizegenetics.pangenome.fastaExtraction: Class which holds various utilities for extracting fastas Created by zrm22 on 2/8/18.

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