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HapCallingUtils - class in net.maizegenetics.pangenome.hapCalling

Created by zrm22 on 8/29/17.

HapCountBestPathPlugin - class in net.maizegenetics.pangenome.hapCalling

 

HapCountBestPathToTextPlugin - class in net.maizegenetics.pangenome.hapCalling

This plugin processes haplotype node data either from of an inclusion file, or from PHG database tables.

hapCountMethod() - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin

Method name used to create haplotype counts, as stored in db table methods

hapCountMethod(String) - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin

Set Hap Count Method.

hapCountMethod() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin

hapCountMethod(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

Set Hap Count Method.

hapDivergence() - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin

Percent each haplotype sequence should diverge from reference

hapDivergence(Integer) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin

Set Haplotype Divergence.

hapidCountMap(Map) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

hapids() - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

List of haplotype ids to include in the graph.

hapids(SortedSet) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Set Haplotype Ids.

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

List of haplotype ids to include in the graph.

hapids(SortedSet) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Set Haplotype Ids.

hapidSetFromReadMappings(Map) - function in net.maizegenetics.pangenome.api.RMethods

 

hapidTableAsDF(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.RMethods

 

hapidTableAsMatrix(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.RMethods

 

haplotypeCountsId() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

DB assigned haplotype_counts_id from the haplotype_counts table.

haplotypeCountsId(Integer) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Hap Counts Id.

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

 

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

 

HaplotypeEdge - class in net.maizegenetics.pangenome.api

 

HaplotypeGraph - class in net.maizegenetics.pangenome.api

This Class is a wrapper around a complete Practical Haplotype Graph (PHG).

Haplotypegraph - class in net.maizegenetics.pangenome.io

 

Haplotypegraph.GVCFIDToFileProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.GVCFIDToFileProto

Haplotypegraph.GVCFIDToFileProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

Protobuf type net.maizegenetics.pangenome.io.GVCFIDToFileProto

Haplotypegraph.GVCFIDToFileProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

Haplotypegraph.HaplotypeEdgeProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.HaplotypeEdgeProto

Haplotypegraph.HaplotypeEdgeProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

Protobuf type net.maizegenetics.pangenome.io.HaplotypeEdgeProto

Haplotypegraph.HaplotypeEdgeProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

Haplotypegraph.HaplotypeGraphProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.HaplotypeGraphProto

Haplotypegraph.HaplotypeGraphProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

Protobuf type net.maizegenetics.pangenome.io.HaplotypeGraphProto

Haplotypegraph.HaplotypeGraphProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

Haplotypegraph.HaplotypeNodeProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.HaplotypeNodeProto

Haplotypegraph.HaplotypeNodeProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

Protobuf type net.maizegenetics.pangenome.io.HaplotypeNodeProto

Haplotypegraph.HaplotypeNodeProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

Haplotypegraph.HaplotypeSequenceProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.HaplotypeSequenceProto

Haplotypegraph.HaplotypeSequenceProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

Protobuf type net.maizegenetics.pangenome.io.HaplotypeSequenceProto

Haplotypegraph.HaplotypeSequenceProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

Haplotypegraph.ReferenceRangeProto - class in net.maizegenetics.pangenome.io.Haplotypegraph

Protobuf type net.maizegenetics.pangenome.io.ReferenceRangeProto

Haplotypegraph.ReferenceRangeProto.Builder - class in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

Protobuf type net.maizegenetics.pangenome.io.ReferenceRangeProto

Haplotypegraph.ReferenceRangeProtoOrBuilder - class in net.maizegenetics.pangenome.io.Haplotypegraph

 

HaplotypeGraphBuilderPlugin - class in net.maizegenetics.pangenome.api

 

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

Name of method to be stored in db

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

Set methodName

HaplotypeNode - class in net.maizegenetics.pangenome.api

 

HaplotypeNode.VariantInfo - class in net.maizegenetics.pangenome.api.HaplotypeNode

These will be instantiated only when requested.

HaplotypePath - class in net.maizegenetics.pangenome.api

Created on June 20, 2017

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

 

HaplotypesDataMetricsPlugin - class in net.maizegenetics.pangenome.pipelineTests

Code to provide metrics on PHG haplotypes based on user supplied method.

HaplotypesDataVectors - class in net.maizegenetics.pangenome.pipelineTests

Class that holds data for haplotypes in a graph in vector form

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

HaplotypeSequence object containing the nucleotide sequence and other sequence related information for a given HaplotypeNode object.

HaplotypeSequence - class in net.maizegenetics.pangenome.api

 

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

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder

 

hasField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder

 

hasHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

.net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;

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

.net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;

hasHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProtoOrBuilder

.net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;

hashCode() - function in net.maizegenetics.pangenome.api.ReferenceRange

 

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

 

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

 

hashCode() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

hashCode() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

hashCode() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

hashCode() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

hashCode() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

hasListeners() - function in net.maizegenetics.plugindef.AbstractPlugin

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.GeneratedMessageV3

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder

 

hasOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder

 

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

 

hostname() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin

Hostname where database resides

hostname(String) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin

Set Hostname.

hostname() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin

Hostname where database resides

hostname(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin

Set Hostname.

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