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A

addAllGvcfIdToFile(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addAllHaplotypeEdges(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addAllHaplotypeNodes(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addAllMethods(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

repeated string methods = 6;

addAllReferenceRanges(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addAllTaxa(Iterable) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder

repeated string taxa = 3;

addGvcfIdToFile(int,Haplotypegraph.GVCFIDToFileProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addGvcfIdToFile(int,Haplotypegraph.GVCFIDToFileProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addGvcfIdToFile(Haplotypegraph.GVCFIDToFileProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addGvcfIdToFile(Haplotypegraph.GVCFIDToFileProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addGvcfIdToFileBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addGvcfIdToFileBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;

addHaplotypeEdges(int,Haplotypegraph.HaplotypeEdgeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeEdges(int,Haplotypegraph.HaplotypeEdgeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeEdges(Haplotypegraph.HaplotypeEdgeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeEdges(Haplotypegraph.HaplotypeEdgeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeEdgesBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeEdgesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;

addHaplotypeNodes(int,Haplotypegraph.HaplotypeNodeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addHaplotypeNodes(int,Haplotypegraph.HaplotypeNodeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addHaplotypeNodes(Haplotypegraph.HaplotypeNodeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addHaplotypeNodes(Haplotypegraph.HaplotypeNodeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addHaplotypeNodesBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addHaplotypeNodesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;

addInGQBlockHeader(Set) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils

 

addInIndels(ReferenceRange,GenomeSequence,List,List,int,FillIndelsIntoConsensus.INDEL_MERGE_RULE) - function in net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus

Method to add in the indels which were removed for the merging process.

addListener(PluginListener) - function in net.maizegenetics.plugindef.AbstractPlugin

 

addMethods(String) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

repeated string methods = 6;

addMethodsBytes(ByteString) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

repeated string methods = 6;

addMissingSequenceNodes(TreeMap) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

 

addMissingSequenceNodes(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

 

addReferenceRanges(int,Haplotypegraph.ReferenceRangeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addReferenceRanges(int,Haplotypegraph.ReferenceRangeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addReferenceRanges(Haplotypegraph.ReferenceRangeProto) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addReferenceRanges(Haplotypegraph.ReferenceRangeProto.Builder) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addReferenceRangesBuilder() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

addReferenceRangesBuilder(int) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;

AddRefRangeAsAssemblyPlugin - class in net.maizegenetics.pangenome.db_loading

This function is fairly obsolete.

AddRefRangeGroupPlugin - class in net.maizegenetics.pangenome.db_loading

This class creates a user defined ref range group, adds it to the specified db, associates requested reference ranges with the new group.

addRepeatedField(Descriptors.FieldDescriptor,Object) - function in com.google.protobuf.GeneratedMessageV3.Builder

 

addRepeatedField(Descriptors.FieldDescriptor,Object) - function in com.google.protobuf.Message.Builder

 

addTaxa(String) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder

repeated string taxa = 3;

addTaxaBytes(ByteString) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder

repeated string taxa = 3;

addToCoordsMap(RangeMap,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

 

adjustEntryForOverlap(String,String,int,Multimap,Multimap,boolean) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

 

adjustment(double) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder

 

alignWithNucmer(String,String,String,String,String,int) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

Call mummer nucmer program to align the sequences Parameters are: -c 250: Set the minimum cluster length to 250 --mum: Use anchor matches that are unique in both the reference and query

all - enum entry in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE

 

all - enum entry in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT

 

allCounts(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability

 

allCounts - enum entry in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD

 

allCounts_oops(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability

 

allCountsWeighted(int,int) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability

 

allCountsWeighted - enum entry in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD

 

AlleleInfo - class in net.maizegenetics.pangenome.api

The AlleleInfo class holds the data for a record coming from the alleles tables in the PHG database.

allTaxonInstance(GenomeSequence,String,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

Method to get a map of taxon to its genome sequence for all the taxon in the vcf file

allTaxonInstance(GenomeSequence,String,boolean) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

Method to get a map of taxon to its genome sequence for all the taxon in the vcf file

altAllele() - function in net.maizegenetics.pangenome.api.Variant

 

altAlleleID() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData

 

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

 

altDepth() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData

 

ANCHOR - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType

 

ANCHOR_HAPLOTYPES - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

AnchorDataPHG - class in net.maizegenetics.pangenome.db_loading

THis class differs from AnchorData in WGS_whatever as it includes more fields to match what is stored in PHGSchema's anchor_haplotypes.

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

 

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

 

AnchorInfo - class in net.maizegenetics.pangenome.trimAnchors

Simple class which holds various information about an anchor.

anchorRegionBed() - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin

Bed File

anchorRegionBed(String) - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin

Set Bed File.

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

 

ancID() - function in net.maizegenetics.pangenome.db_loading.VariantMappingData

 

areGraphTaxaInRankingMap(HaplotypeGraph,Map) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils

Method to verify that the taxa in the graph are in the ranking file.

areRankingsUnique(Map) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils

Method to verify that rankings are unique.

asmBZEnd() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

End position for bz region on the assembly

asmBZEnd(Integer) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Set BZ Assembly End.

asmBZStart() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Start position for bz region on the assembly

asmBZStart(Integer) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Set BZ Assembly Start.

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

 

asmContig() - function in net.maizegenetics.pangenome.api.HaplotypeNode

 

asmContig() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG

 

asmEnd() - function in net.maizegenetics.pangenome.api.HaplotypeNode

 

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

 

asmEnd() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG

 

asmFileId() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG

 

asmStart() - function in net.maizegenetics.pangenome.api.HaplotypeNode

 

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

 

asmStart() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG

 

asmStrand() - function in net.maizegenetics.pangenome.api.HaplotypeNode

 

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

 

asmStrand() - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG

 

assembly() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Assembly fasta file for a single chromosome to align against the reference

assembly(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Set Assembly Fasta File.

assembly() - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin

Output fastq file to use as input for BWA-MEM

assembly(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin

Set Output File.

ASSEMBLY_HAPLOTYPES - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType

 

assemblyFasta() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Assembly fasta file used when aligning

assemblyFasta(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

Set Assembly Genome File.

AssemblyHaplotypesPlugin - class in net.maizegenetics.pangenome.processAssemblyGenomes

This Class is DEPRECATED!!

AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT - class in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

 

assemblyMethod() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Method name to load to db for assembly processing, default is mummer4

assemblyMethod(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Set Assembly Method.

assemblyName() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Name of Assembly Taxon, to be stored as taxon name in the DB

assemblyName(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Set Assembly Name.

AssemblyProcessingUtils - class in net.maizegenetics.pangenome.processAssemblyGenomes

This class contains methods useful for processing assembly haplotypes.

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