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main(Array) - function in net.maizegenetics.pangenome.CompareFastaToReference

 

main(Array) - function in net.maizegenetics.pangenome.CompareHaplotypesToAssembly

 

main(Array) - function in net.maizegenetics.pangenome.GVCFStats

 

main(Array) - function in net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts

 

main(Array) - function in net.maizegenetics.pangenome.GetFastaSequenceLengths

 

main(Array) - function in net.maizegenetics.pangenome.Utils.CreateHashForFiles

 

main(Array) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFile

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

main(Array) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

main(Array) - function in net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts

 

main(Array) - function in net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles

 

main(Array) - function in net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU

 

main(Array) - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes

 

main(Array) - function in net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper

 

main(Array) - function in net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution

 

main(Array) - function in net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs

 

main(Array) - function in net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun

 

main(Array) - function in net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence

 

main(Array) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin

 

main(Array) - function in net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions

 

main(Array) - function in net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG

 

main(Array) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

 

main(Array) - function in net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies

 

main(Array) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

 

main(Array) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

 

main(Array) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin

 

main(Array) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin

 

mainProcessDataJustGenes(String,String,String) - function in net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF

 

mainProcessMergeOverlapsAddGapDifference(String,String,String,int) - function in net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF

 

maxDistance(DistanceMatrix,int,int) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils

Function to figure out what the maximum row and col distance are for a given position in the oringinal distance Matrix.

maxDistFromFounder() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Maximum genetic divergence from founder haplotype to cluster sequences

maxDistFromFounder(Double) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Max divergence from founder.

maxError() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Maximum error allowed to create a homozygous call.

maxError(Double) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Maximum error.

maxNan() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Maximum proportion of Nans allowed in a row of the relationship matrix

maxNan(Double) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Max Nan.

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

maximum number of nodes per reference range.

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

Set Max Nodes.

maxNumberOfClusters() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

The maximum number of clusters allowed.

maxNumberOfClusters(Integer) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Max Clust.

maxNumberOfClusters() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

The maximum number of clusters that will be created for a reference range.

maxNumberOfClusters(Integer) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Maximum Cluster Number.

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

maximum number of include counts per anchor reference range.

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

Set Max Reads.

maxReadsPerRangeKB(int) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

maxThreads() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

The maximum number of threads to be used to create consensi.

maxThreads(Integer) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Max Threads.

mergeCoords(String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

Test method to try to merge overlapping coordinates.

mergeDelimitedFrom(InputStream,ExtensionRegistryLite) - function in com.google.protobuf.AbstractMessageLite.Builder

 

mergeFrom(Message) - function in com.google.protobuf.Message.Builder

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder

 

mergeFrom(Message) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder

 

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

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder

 

mergeFrom(Message) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder

 

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

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder

 

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

 

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

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder

 

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

 

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

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder

 

mergeFrom(Message) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder

 

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

 

mergeFrom(CodedInputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

 

mergeFrom(Message) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

 

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

 

MergeGVCFPlugin - class in net.maizegenetics.pangenome.hapcollapse

Created by zrm22 on 11/6/17.

MergeGVCFUtils - class in net.maizegenetics.pangenome.hapcollapse

Created by zrm22 on 11/7/17.

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

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

mergeRule() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin

The rule in which to resolve the conflicting Indels after consensus has been found.

mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin

Set Indel Merge Rule.

mergeUnknownFields(UnknownFieldSet) - function in com.google.protobuf.AbstractMessage.Builder

 

mergeUnknownFields(UnknownFieldSet) - function in com.google.protobuf.Message.Builder

 

mergeUnknownFields(UnknownFieldSet) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder

 

mergeUnknownFields(UnknownFieldSet) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder

 

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

 

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

 

mergeUnknownFields(UnknownFieldSet) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder

 

mergeUnknownFields(UnknownFieldSet) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder

 

method(ReferenceRangeEmissionProbability.METHOD) - function in net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder

 

methodDetails() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin

Desscription for this group of reference ranges.

methodDetails(String) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin

Set Method Details.

methodId(Connection,String) - function in net.maizegenetics.pangenome.api.CreateGraphUtils

Returns method id (methods.method_id) for given method name.

methodName() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin

Method name for this reference range group.

methodName(String) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin

Set Method Name.

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

Pairs of methods (haplotype method name and range group method name).

methods(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

Set Methods.

methods() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

Pairs of methods (haplotype method name and range group method name).

methods(String) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

Set Methods.

methods() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin

Pairs of methods (haplotype method name and range group method name).

methods(String) - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin

Set Methods.

MethodTableReportPlugin - class in net.maizegenetics.pangenome.api

MethodTableReportPlugin exports the contents of the PHG db method table to a table report.

minAlleleFrequency() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

At each position, if no allele has the minimum frequency, the consensus haplotype allele will be set to misssing.

minAlleleFrequency(Double) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Minimum Allele Frequency.

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

Minimun number of taxa represented in reference range for reference range to remain in graph

minCountTaxa(Integer) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Set Min Count Taxa.

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

Minimum length of inversion for it to be kept as part of the alignment.

minInversionLen(Integer) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Set Minimum Inversion Length.

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

Minimum percent of taxa represented in reference range for reference range to remain in graph.

minPercentTaxa(Double) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

Set Min Percent Taxa.

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

Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,

minProbBF(Double) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Min P.

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

minimum number of reads per anchor reference range.

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

Set Min Reads.

minReadsPerRange(int) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

minSiteForComp() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering

minSiteForComp(Integer) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Min sites to cluster.

minSiteForComp() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

The minimum number of shared sites that can be used to calculate the distance between two taxa

minSiteForComp(Integer) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Minimum Sites with Data .

minTaxa() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Minimum number of taxa

minTaxa(Integer) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Min Taxa.

minTaxaCoverage() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

The minimum proportion of sites present in a taxa to go into clustering

minTaxaCoverage(Double) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Min taxa coverage.

minTaxaCoverage() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Minimum Coverage

minTaxaCoverage(Double) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Minimum Coverage.

minTaxaInGroup() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Minimum number of taxa to generate a haplotype

minTaxaInGroup(Integer) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Set Min taxa to generate a haplotype.

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

minimum number of taxa per anchor reference range.

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

Set Min Taxa.

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

minimum probability of a transition between nodes at adjacent reference ranges.

minTransitionProb(Double) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Min Transition Prob.

minTransitionProbability(double) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

mostCommonHaplotype - enum entry in net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE

 

mostCommonHaplotypesAsHet - enum entry in net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE

 

Mummer4DoonerBZStats - class in net.maizegenetics.pangenome.processAssemblyGenomes

This method takes a coords file, the genome fastas, ranges to be covered Prints out tab-delimited file of metrics related to the region.

mummer4Path() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Path to mummer4 binaries

mummer4Path(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

Set Mummer4 binary path

MummerAnalysisMetricsPlugin - class in net.maizegenetics.pangenome.processAssemblyGenomes

This method provides summary statistics on mummer output.

mummerParams() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

Mummer parameters used

mummerParams(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

Set Mummer Parameters.

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

Parameters used when running mummer

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

Set Mummer Parameters.

MummerScriptProcessing - class in net.maizegenetics.pangenome.processAssemblyGenomes

This class contains methods that run mummer4 scripts, e.g.

mxDiv() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Maximum divergence.

mxDiv(Double) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

Set Mx Div.

myPairedSimilarFragmentSort(List,int,int,int) - function in net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors

 

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