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P

PairedSimilarFragment - class in net.maizegenetics.pangenome.processAssemblyGenomes

Class that holds reference and assembly alignment data to be sorted and filtered in a longest path algorithm.

parseBauerFlint(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

parseChromAsRomanNumerals(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

parseChromFirstTab(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

parseChromosome(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

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

Method to parse out the reference coordinates into a map which along with the SNP data can then be used to create Variants.

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

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

 

parseDelimitedFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto

 

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

 

parseFrom(Array,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

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

 

parseFrom(ByteString,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

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

 

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

 

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

 

parseFrom(InputStream,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

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

 

parseFrom(ByteBuffer,ExtensionRegistryLite) - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto

 

parseGCA(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

parseMethodJsonParamsToString(String) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils

Takes a passed method description string from a PHG dd methods table entry, and formats the JSON key/value pairs into a Mapfor the user.

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

Method to parse the Mummer SNP file into a rangemap The first String in the tuple is for the reference call The second String is for the assembly call

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

 

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

 

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

 

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

 

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

 

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

 

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

Password for database

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

Set Password.

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

Password for database

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

Set Password.

path(TreeMap) - function in net.maizegenetics.pangenome.api.GraphUtils

Returns sorted set of haplotype ids from the given paths.

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

Returns most probable HaplotypePath for each Chromosome.

path(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns most probable HaplotypePath for each Chromosome given the specified taxon.

path(String,List) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes.

path(List) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns most probable HaplotypePath for each Chromosome given the specified list of known s.

path(Taxon) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns most probable HaplotypePath for each Chromosome given the specified Taxon.

path(Taxon,List) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns most probable HaplotypePath for each Chromosome given the specified Taxon and list of known HaplotypeNodes.

pathHapids(String,Array) - function in net.maizegenetics.pangenome.api.RMethods

 

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

The name of the file to which detailed path diagnostic information will be written.

pathInfoFilename(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

Set Path Info File.

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

Name of method used to create paths, as it should appear in the paths table

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

Set Path Method.

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

Name of method to be used to create paths through the graph.

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

Set P Method.

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

Description of method used to create paths - optional

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

Set Path Method Details.

pathMethodName() - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin

Path Method Name Stored in the DB

pathMethodName(String) - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin

Set Path Method Name.

pathMethodName() - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin

Path Method Name Stored in the DB

pathMethodName(String) - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin

Set Path Method Name.

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

Name of method used for create PHG Path.

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

Set Path Method Name.

pathName() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

The path method name assigned when the path was created and stored in the DB.

pathName(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

Set Path method name.

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

 

pathsDir() - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin

Paths directory

pathsDir(String) - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin

Set Paths Directory.

pathsForMethod(String,String) - function in net.maizegenetics.pangenome.api.RMethods

 

pathsToNodes(TreeMap) - function in net.maizegenetics.pangenome.api.GraphUtils

 

PathToIgraphPlugin - class in net.maizegenetics.pangenome.hapCalling

 

performFunction(DataSet) - function in net.maizegenetics.plugindef.AbstractPlugin

 

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

 

PHGData - class in net.maizegenetics.pangenome.db_loading

 

PHGDataWriter - class in net.maizegenetics.pangenome.db_loading

 

PHGdbAccess - class in net.maizegenetics.pangenome.db_loading

Access methods for postgres or SQL PHG dbs.

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

 

pluginDescription() - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin

 

pluginDescription() - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin

 

pluginDescription() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

 

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

 

pluginDescription() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

 

pluginDescription() - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin

 

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

 

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

 

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

 

pluginUserManualURL() - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

 

pluginUserManualURL() - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin

 

pluginUserManualURL() - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin

 

pluginUserManualURL() - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin

 

pluginUserManualURL() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

 

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

 

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

 

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

 

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

 

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

Name to prefix to output results file

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

Set Output File refix.

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

Name to prefix to output results file

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

Set Output File refix.

presenceAbsenceTaxonByNode(HaplotypeGraph,String) - function in net.maizegenetics.pangenome.api.GraphUtils

 

previousRange(ReferenceRange) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

 

printTrimTables(String,String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

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

 

probabilityOfBeingCorrect(Multiset,TreeMap) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

probabilityOfBeingCorrect(Map,TreeMap) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

probabilityOfBeingCorrect(HaplotypeGraph,Multiset) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

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

 

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

minimum number of reads per anchor reference range.

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

Set Prob Correct.

processCreateHash(String,String) - function in net.maizegenetics.pangenome.Utils.CreateHashForFiles

 

processData(DataSet) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.gui.ViewGraphPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

Plugin method to process the data

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Method to create a consensus haplotype GenotypeTable object Method will now just create and return the GenotypeTable instead of doing additional work to create the fasta sequence.

processData(DataSet) - function in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin

 

processData(String,String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin

 

processData(DataSet) - function in net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin

 

processDecimal(int,int,int) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

 

processHaplotypesData(int,int,Map,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

 

processMain(String,String,String) - function in net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading

 

processMain(String,String,String) - function in net.maizegenetics.pangenome.db_loading.CreateIntervalsFile

 

processMain(String,Map,String,String) - function in net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates

 

processMain(String,Map,String,String) - function in net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates

 

processMain(String,String,String,String) - function in net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes

 

progress(PluginEvent) - function in net.maizegenetics.plugindef.AbstractPlugin

 

PurgeSequencesFromAlignments - class in net.maizegenetics.pangenome.hapcollapse

Created by edbuckler on 6/19/17.

putAllAnchors(List,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file

putAllAnchors(List,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file

putAssemblyInterAnchorSequences(String,int,String,Multimap) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table.

putAssemblyInterAnchorSequences(String,int,String,Multimap) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table.

putConsensusSequences(Multimap,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

This method takes a map of consensus data, finds the anchorIds based on Position, finds the hapids of the taxa whose sequences at the specified anchorID map to the consensus.

putConsensusSequences(Multimap,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

This method takes a map of consensus data, finds the anchorIds based on Position, finds the hapids of the taxa whose sequences at the specified anchorID map to the consensus.

putGameteGroupAndHaplotypes(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists

putGameteGroupAndHaplotypes(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists

putGenoAndHaploTypeData(GenoHaploData) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Stores required data to the genotypes and haplotypes tables for each entry on the list.

putGenoAndHaploTypeData(GenoHaploData) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Stores required data to the genotypes and haplotypes tables for each entry on the list.

putGenomeFileData(String,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.

putGenomeFileData(String,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.

putHalotypeListData(List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

put data to the haplotype Lists table.

putHalotypeListData(List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

put data to the haplotype Lists table.

putHaplotypeCountsData(String,Map,String,String,Array) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

This method adds data to the haplotype_counts table.

putHaplotypeCountsData(String,Map,String,String,Array) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

This method adds data to the haplotype_counts table.

putHaplotypesData(int,int,Map,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId.

putHaplotypesData(int,int,Map,String,int,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries.

putHaplotypesData(int,int,Map,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId.

putHaplotypesData(int,int,Map,String,int,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries.

putHaplotypesForGamete(int,int,Map,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in.

putHaplotypesForGamete(int,int,Map,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in.

putHaplotypesForMultipleGroups(Multimap,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Add data to the haplotypes table.

putHaplotypesForMultipleGroups(Multimap,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Add data to the haplotypes table.

putMethod(String,DBLoadingUtils.MethodType,Map) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created.

putMethod(String,DBLoadingUtils.MethodType,Map) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created.

putPathsData(String,Map,String,List,Array,boolean) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

This method stores paths data to the paths table.

putPathsData(String,Map,String,List,Array,boolean) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

This method stores paths data to the paths table.

putReadMappingData(String,Map,String,String,Array,boolean,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data.

putReadMappingData(String,Map,String,String,Array,boolean,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data.

putRefAnchorData(String,int,List,int,Set,String,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Fills in the haplotypes table for the reference ranges.

putRefAnchorData(String,int,List,int,Set,String,String,int,int) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Fills in the haplotypes table for the reference ranges.

putRefRangeRefRangeMethod(int,List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a method id and a list of reference ranges.

putRefRangeRefRangeMethod(int,List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a method id and a list of reference ranges.

putTaxaGroupName(String) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Creates an entry in the taxa_groups table.

putTaxaGroupName(String) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Creates an entry in the taxa_groups table.

putTaxaTaxaGroups(String,List) - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter

Takes a taxa group name and a list of taxa.

putTaxaTaxaGroups(String,List) - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess

Takes a taxa group name and a list of taxa.

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