Index (net.maizegenetics:phg 0.0.1 API)

A B C D E F G H I K L M N O P Q R S T U V W

A

addInIndels(ReferenceRange, GenomeSequence, List<List<VariantContext>>, List<List<VariantContext>>, int, FillIndelsIntoConsensus.INDEL_MERGE_RULE) - Static method in class net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus: Method to add in the indels which were removed for the merging process.
addInnerAnchorNodes(TreeMap<ReferenceRange, List<HaplotypeNode>>, Connection, Map<Integer, ReferenceRange>, Map<Integer, TaxaList>, boolean, int) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
addMissingSequenceNodes(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
addMissingSequenceNodes(TreeMap<ReferenceRange, List<HaplotypeNode>>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
addToCoordsMap(RangeMap<Integer, String>, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
addUnconsolidatedNodes(Connection, Map<ReferenceRange, List<HaplotypeNode>>, Map<Integer, ReferenceRange>, Map<Integer, TaxaList>, boolean) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.
adjustEntryForOverlap(String, String, int, Multimap<Integer, String>, Multimap<Integer, String>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
adjustment(double) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
alignmentFiltered - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
alignmentRaw - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
alignWithNucmer(String, String, String, String, String, int) - Static method in class 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
allCounts(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
allCounts_oops(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
allCountsWeighted(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
allTaxonInstance(GenomeSequence, String, boolean) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence: Method to get a map of taxon to its genome sequence for all the taxon in the vcf file
alternativeSeqFile - Static variable in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
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.
AnchorDataPHG(Range<Position>, Range<Position>, String, byte[], String, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
anchorEnd() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
anchorFile() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: File with list of anchors.
anchorFile(String) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Anchor File.
anchorId() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
anchorIDFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
anchorIDFile - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
AnchorInfo - Class in net.maizegenetics.pangenome.trimAnchors: Simple class which holds various information about an anchor.
AnchorInfo(int, String, int, int, int, int) - Constructor for class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
AnchorInfo(int, String, int, int, int, int, int, int) - Constructor for class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
anchorRegionBed() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin: Bed File
anchorRegionBed(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin: Set Bed File.
anchors() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Tab-delimited file containing chrom, start position, end position
anchors(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Set Anchors File.
anchorStart() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
asmBZEnd() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: End position for bz region on the assembly
asmBZEnd(Integer) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set BZ Assembly End.
asmBZStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Start position for bz region on the assembly
asmBZStart(Integer) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set BZ Assembly Start.
assembly() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Assembly fasta file for a single chromosome to align against the reference
assembly(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Assembly Fasta File.
assembly() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Output fastq file to use as input for BWA-MEM
assembly(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Set Output File.
assemblyFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Assembly fasta file used when aligning
assemblyFasta(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Assembly Genome File.
AssemblyHaplotypesPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes: Process Assemblies - both anchor and interanchor.
AssemblyHaplotypesPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
AssemblyHaplotypesPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
AssemblyHaplotypesPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
assemblyName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Name of Assembly Taxon, to be stored as taxon name in the DB
assemblyName(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Assembly Name.
AssemblyProcessingUtils - Class in net.maizegenetics.pangenome.processAssemblyGenomes: This class contains methods useful for processing assembly haplotypes.
AssemblyProcessingUtils() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

B

bamFile() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: File Name of the bam file
bamFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: Set Bam File.
basicConverterTest() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
bedFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Name for the bed file
bedFile(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Set Bed File.
bedFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: File holding the Reference Range Information
bedFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Set Bed File.
bedFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Bed file containing the gene information.
bedFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Bed File.
bfInfoFilename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The name of the file to node probabilities from the backward-forward algorithm will be written.
bfInfoFilename(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Bf Info File.
build() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
build() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
Builder() - Constructor for class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
buildHaplotypeGraph() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils

C

calcLevenshtein(String, String, int) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
calculateCoordDistance(Tuple<Integer, Integer>, Tuple<Integer, Integer>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Calculates distance between 2 sets of mummer coords file entries This is called on coordinates that are both either ascending (start < end) or both descending (start > end) so "sign" of entries is not checked here.
callSNPsFromHaplotypeNodes(List<HaplotypeNode>, HashMap<Integer, String>, String, String, String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
callSNPsFromHaplotypePath(HaplotypeGraph, HaplotypePath, String, String, String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
callSNPsFromSomeVCFs(String, String, String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
checkChrom2DupAnchor(String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
checkForEmbedded(List<String>, boolean) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Check entries in a list of mummer4 coords file entries and removed those that are embedded
checkForOverlap(Tuple<Integer, Integer>, Tuple<Integer, Integer>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Returns a Tuple indicating THe original list was sorted, so prevStartEnd.x will be <= curStartEnd.x
checkForSeqMatch(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
checkNoListEntriesInRange(HashSet<Integer>, List<Integer>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Method takes a RangeSet of Integers and a list of integers.
checkSnpEntryInRange(String, RangeMap<Position, List<Position>>, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Verifies if the positions from a Mummer4 snp file fall within the range map of reference and assembly positions created from the Mummer4 coordinates files.
chooseBestNode(HaplotypeGraph, Multiset<Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
chrom() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: If a chrom is specified, pull only data for that chromosome.
chrom(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Chrom.
chrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
chrom(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Chromosome Name.
chrom() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
chromosome() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: Chromosome in the reference genome from which this ReferenceRange originates
chromosomes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
chromosomes() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSequence(Chromosome) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Unsupported method to get the sequence for the whole chromosome
chromosomeSequence(Chromosome, int, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
chromosomeSequence(Chromosome) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSequence(Chromosome, int, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSize(Chromosome) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
close() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
CloseDBConnectionPlugin - Class in net.maizegenetics.pangenome.db_loading: This method closes a DB connection.
CloseDBConnectionPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
CloseDBConnectionPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
CloseDBConnectionPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
clusterMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: The method used to cluster taxa.
clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Cluster Method.
clusterMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: The method used to cluster taxa.
clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Cluster Method.
clusterSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Cluster size to use with mummer4 nucmer script.
clusterSize(Integer) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Mummer4 Nucmer Cluster Size .
collapseMethod() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Name of method used to collapse the anchors.
collapseMethod(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Set Collapse Method.
collapseMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Name of the collapse method to be stored in the database
collapseMethod(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Collapse Method.
collapseMethodDetails() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Details for the collapse method to be stored in the database
collapseMethodDetails(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Collapse Method Details.
comparaRawFilteredAlignment(String, String) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
CompareAssembliesToReference - Class in net.maizegenetics.pangenome.hapcollapse: Simple little utility to compare assembly alignments to the reference genome
CompareAssembliesToReference() - Constructor for class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
CompareFastaToReference - Class in net.maizegenetics.pangenome: Created by terry on 3/21/17.
CompareFastaToReference() - Constructor for class net.maizegenetics.pangenome.CompareFastaToReference
CompareHaplotypesToAssembly - Class in net.maizegenetics.pangenome: Created by terry on 3/21/17.
CompareHaplotypesToAssembly() - Constructor for class net.maizegenetics.pangenome.CompareHaplotypesToAssembly
compareRefToReAssembledChrom(String, String, String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
compareTo(HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
compareTo(ReferenceRange) - Method in class net.maizegenetics.pangenome.api.ReferenceRange
compareTo(AnchorDataPHG) - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
compareTo(GeneGFFData) - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
CompareToKnownSNPPlugin - Class in net.maizegenetics.pangenome.pipelineTests: Plugin to compare A GenotypeTable to a known trusted GenotypeTable Inputs: -DataSet of at least 2 GenotypeTables, First one is the known SNP set you wish to compare to, the rest are compared in order.
CompareToKnownSNPPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
ComputeMedianAnnotation - Class in net.maizegenetics.pangenome.gvcfFiltering: Simple Utility to Extract Mean, Median and Mode for Depth in a GVCF file Currently supports only DP as defined in the FORMAT Tag.
ComputeMedianAnnotation() - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
ComputeMedianGVCFAndFilter - Class in net.maizegenetics.pangenome.gvcfFiltering: TODO Separate Filter from FastaExtraction Created by zrm22 on 7/18/17.
ComputeMedianGVCFAndFilter() - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
ComputeNDistribution - Class in net.maizegenetics.pangenome.multiSequenceAlignment: Simple One off Main class to compute how many Ns we have over all the basepairs of all the anchors TODO if needed in pipeline, Refractor into TASSEL code Created by zrm22 on 5/25/17.
ComputeNDistribution() - Constructor for class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
configFile() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Database configuration file
configFile(String) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Database Config File.
configFile() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: Set DB Config Files.
configFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Name of config file to use for db connection
configFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Set DB Config File.
configFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Config folder containing the filtering parameters.
configFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Config File.
configFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Config folder containing the filtering parameters.
configFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Set Config File.
configFile - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
configFile() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Config file that specifies database connection parameters
configFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Config File.
configFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: ConfigFile name
configFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set ConfigFile Name.
configFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Database configuration file
configFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Database Config File.
configFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Database configuration file
configFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Database Config File.
configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set DB Config File.
configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set DB Config File.
configFileName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
connection(String) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates a database connection given a properties file
connection(String, String, String, String) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates a Postgres database connection.
connection(String, boolean) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils: Creates a database connection given a properties file It is expected that only initial db loading methods will call this with "createNew" = true.
connection(String, String, String, String, String, boolean) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils: Creates a new database connection or returns connection to existing db If createNew is FALSE then try to connect, and if db doesn't exist, return NULL NOTE: from postgres, User should never create a db that matches all lower case to an existing db.
consensusFastaOutputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Directory where you want to store the output fastas from the consensus process
consensusFastaOutputDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Consensus Fasta Output Dir.
consensusHaplotypes - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
consensusVCFOutputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Directory where you want to store the output VCFs from the consensus process
consensusVCFOutputDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Consensus VCF Output Dir.
contains(String, TaxaList) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
containsW22(TaxaList) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
contigBAM() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Name of contig BAM file to process
contigBAM(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Contig File.
ContrastHaplotypeAndAssemblySequence - Class in net.maizegenetics.pangenome.pipelineTests: Integration test to evaluate fasta file generated from GVCF files for the whole genome against assembly fasta Assembly fasta Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (W22).
ContrastHaplotypeAndAssemblySequence() - Constructor for class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
convertCSVToBed(String[]) - Static method in class net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
convertCSVToIntervals(String[]) - Static method in class net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
ConvertGBSToSNPs - Class in net.maizegenetics.pangenome.hapCalling
ConvertGBSToSNPs() - Constructor for class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
ConvertGBSUtils - Class in net.maizegenetics.pangenome.hapCalling
ConvertGBSUtils() - Constructor for class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
ConvertRampSeqTagsToMapPlugin - Class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 10/4/17.
ConvertRampSeqTagsToMapPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
ConvertToHaplotypeCallerInput - Class in net.maizegenetics.pangenome
ConvertToHaplotypeCallerInput() - Constructor for class net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
convertVCFToGVCF(List<VariantContext>) - Static method in class net.maizegenetics.pangenome.hapcollapse.GVCFUtils
coordsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Output of Mummer coords file
coordsFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Mummer Coords File.
coordsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Output of Mummer coords file
coordsFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Mummer Coords File.
CountConsensusTaxaAtRefRange - Class in net.maizegenetics.pangenome.pipelineTests: This class counts the number of taxa represented at each genome_interval region based on the method supplied.
CountConsensusTaxaAtRefRange() - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
CountConsensusTaxaAtRefRange(Frame) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
CountConsensusTaxaAtRefRange(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
countHaplotypeNodesFromFastQ() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
countMethod() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The haplotype count method name assigned when the counts were created and stored in the DB.
countMethod(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Haplotype count method name.
countNodesWithW22(List<HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
countNsInFasta() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
CountNsInRawHapSequencesPlugin - Class in net.maizegenetics.pangenome.pipelineTests: Calculates the percentage of N's for each "raw" haplotype (ie, not consensus) for each genome interval (anchor, not inter-anchors).
CountNsInRawHapSequencesPlugin() - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
CountNsInRawHapSequencesPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
CountNsInRawHapSequencesPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
countSeqCharInPHG() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
countW22NodesFullGraph(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
CreateAnchorFilesFromGeneGFF - Class in net.maizegenetics.pangenome.db_loading: Based on WGS_whatever.CreateAnchorsFromGeneGff.java This method creates two fasta files of anchor coordinates: The first has exact gene coordinates to be used when blasting B73 reference genes against a particular assembly, e.g.
CreateAnchorFilesFromGeneGFF() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
createAndLoadAssemblyData(Map<Integer, ReferenceRange>, List<VariantContext>, GenomeSequence, Connection, String, String, String, int) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Create the assembly genotype/haplotype data and load to the PHG database
CreateBiggerIntervals - Class in net.maizegenetics.pangenome.db_loading
CreateBiggerIntervals() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals
CreateContigFastaFromAssemblyGenomePlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes: The sequence for each chromosome in the genome fasta file will be split based on N's.
CreateContigFastaFromAssemblyGenomePlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
CreateContigFastaFromAssemblyGenomePlugin(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
CreateContigFastaFromAssemblyGenomePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
CreateCSV_TrimmedAnchorLoading - Class in net.maizegenetics.pangenome.db_loading: This method takes as input 2 csv files It takes the data from FindTrimmedAnchorCoordinates.jar, then calculates new coordinates using the old ref coordinates CSV file used for loading.
CreateCSV_TrimmedAnchorLoading() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
CreateDBLoadScripts - Class in net.maizegenetics.pangenome.fastaExtraction: Simple Main program to create the script used to load all of the haplotype_caller fastas into the db TODO Refractor the logic and move execution to a plugin Created by zrm22 on 5/12/17.
CreateDBLoadScripts() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
createEdges(Collection<HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Generates Edges based on HaplotypeNodes.
createEdges(TreeMap<ReferenceRange, List<HaplotypeNode>>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Generates Edges based on HaplotypeNodes.
CreateFastaDBFiles - Class in net.maizegenetics.pangenome.fastaExtraction: Simple one off command line tool to create the necessary files to upload fastas to the db.
CreateFastaDBFiles() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
createFiles(String, String) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
createFindProteomeFile() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
createGenotypeTableFromGVCFs(ReferenceRange, Multimap<Taxon, VariantContext>, GenomeSequence) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
createGenotypeTableFromHaplotypeNodes(ReferenceRange, List<HaplotypeNode>, GenomeSequence) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: Method to make a genotypeTable from a list of Haplotype Nodes.
CreateGraphUtils - Class in net.maizegenetics.pangenome.api
createHapIdToFileNameMapping(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
createHaplotypeNodeList(String, String) - Static method in class net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
createHaplotypeNodeListFromDirectory(String, String) - Static method in class net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
CreateHaplotypeNodeListFromFasta - Class in net.maizegenetics.pangenome.api: Simple class to create a haplotype node list from a set of or a single fasta file Created by zrm22 on 8/14/17.
CreateHaplotypeNodeListFromFasta() - Constructor for class net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
createHaplotypeNodes(Connection, Map<Integer, ReferenceRange>, Map<Integer, TaxaList>, String, boolean, boolean, SortedSet<Integer>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates lists of HaplotypeNodes organized by reference Range based on the given method.
createHaplotypeNodes(Connection, String, boolean, boolean, SortedSet<Integer>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates HaplotypeNode Lists with keys as ReferenceRanges.
createHaplotypeNodesWithVariants(Connection, Set<HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.
createHaplotypeNodesWithVariants(Connection, HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.
CreateHaplotypesFromFasta - Class in net.maizegenetics.pangenome.hapcollapse: Created by edbuckler on 6/19/17.
CreateHaplotypesFromFasta() - Constructor for class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
CreateHashForFiles - Class in net.maizegenetics.pangenome.Utils: This class creates the MD4 or SHA-1 hash for a specified file.
CreateHashForFiles() - Constructor for class net.maizegenetics.pangenome.Utils.CreateHashForFiles
createInbredFiles(String, String) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
CreateIntervalBedFilesPlugin - Class in net.maizegenetics.pangenome.db_loading: Created by zrm22 on 1/16/18.
CreateIntervalBedFilesPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
CreateIntervalsFile - Class in net.maizegenetics.pangenome.db_loading: This method must be re-worked - getHaplotypeAnchorCoordinates no longer accesses the correct tables.
CreateIntervalsFile() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
CreateIntervalsFileFromGffPlugin - Class in net.maizegenetics.pangenome.db_loading: This class creates the interval files needed for running GATK haplotype caller, and the csv files needed for loading reference sequence into the database.
CreateIntervalsFileFromGffPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
CreateIntervalsFileFromGffPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
CreateIntervalsFileFromGffPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
createLoadScript(String, String, String, String, String, String) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts: Method which will create the loading script based on the input files.
createNew() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: True indicates a new DB of this name should be created, deleting any existing DB of this name.
createNew(Boolean) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: Set Create New DB.
CreatePHGPostgresDockerPlugin - Class in net.maizegenetics.pangenome.db_loading: This plugin will create the phg_postgres docker if it doesn't exist.
CreatePHGPostgresDockerPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
CreatePHGPostgresDockerPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
CreatePHGPostgresDockerPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
createRefRangeGroup(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: Creates an entry in the ref_range_groups table using method_id associated with the name indicated via the method parameter.
createRefRangeGroup(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
createSHA1Hash(String) - Static method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
CreateStreamGraph - Class in net.maizegenetics.pangenome.gui
createTrimmedFastaGenotypeTable(String, String, double, double, int, int, int, int) - Static method in class net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors: Method which will create a trimmed GenotypeTable based on the gene start and end positions
createTrimmedFastaGenotypeTable(String, String, String, int, double, double, int, int, int, int) - Static method in class net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors: Method which will create a trimmed GenotypeTable based on the gene start and end positions

D

databaseName() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Database name
databaseName(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Database Name.
databaseName() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Database name
databaseName(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Set Database Name.
databaseName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Database name
databaseName(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Database Name.
dBConfig() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Config file used to set up the db connection
dBConfig(String) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Set Db Config.
dbConfigFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: File holding the DB config information
dbConfigFile(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Set Db Config File.
dbConfigFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: File holding the DB config information
dbConfigFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Set Db Config File.
dbConfigFile() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: File holding the DB config information
dbConfigFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Db Config File.
dbConfigFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
dbConfigFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set DB Config File.
DBLoadingUtils - Class in net.maizegenetics.pangenome.db_loading: Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs.
DBLoadingUtils() - Constructor for class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
DBLoadingUtils.AnchorType - Enum in net.maizegenetics.pangenome.db_loading
DBLoadingUtils.MethodType - Enum in net.maizegenetics.pangenome.db_loading
debugTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Debug taxon
debugTaxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Debug Taxon.
debugTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Debug taxon
debugTaxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Debug Taxon.
decodeByteArrayToListOfVariantContext(byte[]) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
decodeHapCountsArray(byte[]) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
decodePathsArray(byte[]) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
distanceAllTaxaToGivenTaxa(DistanceMatrix, String) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
distanceTaxaPair(DistanceMatrix, String, String) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
distributionTaxaRepresented(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
dockerCmd() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin: The docker command name.
dockerCmd(String) - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin: Set Docker Command.
dockerDir() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin: Directory path where the file 'Dockerfile' exists for creating the PHG Postgresql docker
dockerDir(String) - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin: Set Docker Directory.

E

edge(HaplotypeNode, HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns optional edge between given nodes.
edgeProbability() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge: Probability that the node to the right of this edge HaplotypeEdge.rightHapNode() is the next HaplotypeNode when traversing the graph from left to right.
edges() - Method in class net.maizegenetics.pangenome.api.HaplotypePath: Haplotype Edges that create this HaplotypePath
emissionMethod() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Emission Method
emissionMethod(ReferenceRangeEmissionProbability.METHOD) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Emission Method.
emissionProbabilityMethod(ReferenceRangeEmissionProbability.METHOD) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
emitModeParam() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Emit Mode for running GVCFTyper.
emitModeParam(GVCFTyperPlugin.EMIT_MODE) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Emit_mode.
encodeHapCountsArrayFromFile(String) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeHapCountsArrayFromMultiset(Multiset<HaplotypeNode>, Multiset<HaplotypeNode>) - Static method in class 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.
encodePathArrayFromSet(Set<HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeSelectedVCFRegionsToByteArray(String, boolean, boolean, Range<Position>) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVariantContextListToByteArray(List<VariantContext>, boolean) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVariantContextStreamToByteArray(Stream<VariantContext>, boolean, boolean) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
encodeVCFFileToByteArray(String, boolean, boolean) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
end() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: End position of reference range, inclusive
end() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
endNodes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns list of HaplotypeNodes that end graph.
endNodes(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
equals(Object) - Method in class net.maizegenetics.pangenome.api.ReferenceRange
equals(Object) - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
EvaluateGVCFbyKnownSNPTest - Class in net.maizegenetics.pangenome.pipelineTests: Create unit test to evaluate GVCF SNPs by comparing to known SNPs.
EvaluateGVCFbyKnownSNPTest() - Constructor for class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
EvaluateGVCFbyKnownSNPTest2 - Class in net.maizegenetics.pangenome.pipelineTests: Create unit test to evaluate GVCF SNPs by comparing to known SNPs.
EvaluateGVCFbyKnownSNPTest2() - Constructor for class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
EvaluateGVCFWithIBDTest - Class in net.maizegenetics.pangenome.pipelineTests: Evaluate GVCF calls in regions with IBD to the reference genome.
EvaluateGVCFWithIBDTest() - Constructor for class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFWithIBDTest
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).
EvaluateHaplotypeFastaInKnownIBDRegions() - Constructor for class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
evaluateOneBestNodeRanges(HaplotypeGraph, Multiset<Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
exclusionCountMap(Map<Integer, Integer>) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
exportHaplotypeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Text file to store haplotype scoring
exportHaplotypeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Export Haplo File.
exportHaplotypeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Text file to store haplotype scoring
exportHaplotypeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Export Haplo File.
ExportHaplotypePathToFilePlugin - Class in net.maizegenetics.pangenome.hapCalling: Plugin to export the Multimap exported by a Path finding algorithm to a directory of text files Created by zrm22 on 10/13/17.
ExportHaplotypePathToFilePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
exportMergedRegions(Map<Range<Position>, List<Position>>, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Deprecated.
ExportVCForTaxonMethodPlugin - Class in net.maizegenetics.pangenome.hapCalling: Exports variant context lists to vcf file.
ExportVCForTaxonMethodPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
ExportVCForTaxonMethodPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
ExportVCForTaxonMethodPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
extendedBedFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Name for the extended bed file
extendedBedFile(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Set Extended Bed File.
extractAnchorVariantContextsFromAssemblyAlignments(GenomeSequence, String, RangeSet<Position>, Map<Range<Position>, List<Position>>, RangeMap<Position, Tuple<String, String>>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method to build the list of VariantContexts based on the mapped coordinates and the SNPs
extractFasta(String, String, String) - Method in class 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.
ExtractFastaFromGVCFCBSU() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU
extractFastaSequence(List<VariantContext>, ReferenceRange) - Static method in class 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.
ExtractFastaUtils() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.ExtractFastaUtils

F

fasta() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: Fasta file containing haplotype sequences
fasta(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: Set Fasta File.
fasta() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Fasta File to split by chromosome
fasta(String) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Set Fasta File .
fastaAlternatives - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
fastqFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Name of fastQ file used in FastqToHapCountPlugin
fastqFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Set Fastq File.
fastqName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The name of the fastq file used to create the path.
fastqName(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Fastq name.
FastqToHapCountPlugin - Class in net.maizegenetics.pangenome.hapCalling: Plugin to run the read counting method based on bwa mem alignment.
FastqToHapCountPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
FastqToKmerCountPlugin - Class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 10/23/17.
FastqToKmerCountPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
FillIndelsIntoConsensus - Class in net.maizegenetics.pangenome.hapcollapse: This class is created to fill in the agreeing indels removed from the consensus haplotypes during the merge process.
FillIndelsIntoConsensus() - Constructor for class net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus
FillIndelsIntoConsensus.INDEL_MERGE_RULE - Enum in net.maizegenetics.pangenome.hapcollapse
filter(HaplotypeGraph) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
filterAndExtractFasta(Path, String, GenomeSequence, String, Properties, boolean, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter: Method to filter the gvcf and extract the fasta using the config file.
filterAndExtractFasta(Path, String, GenomeSequence, String, Tuple<Double, Double>, boolean, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter: Old method using a poissonProbability tuple to filter based on depth.
filterBadAlignments(GenotypeTable, double, int, double) - Static method in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments: This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF
filterCoordsOverlaps(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Takes a mummer coords file and searches for overlaps.
filteredGraph() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
FilterFastqUsingBAMPlugin - Class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 9/13/17.
FilterFastqUsingBAMPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
FilterGraphPlugin - Class in net.maizegenetics.pangenome.api
FilterGraphPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.api.FilterGraphPlugin
filterGVCF(String, String, Properties, boolean, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
FilterGVCFPlugin - Class in net.maizegenetics.pangenome.gvcfFiltering: Created by zrm22 on 10/30/17.
FilterGVCFPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
FilterGVCFSingleFilePlugin - Class in net.maizegenetics.pangenome.gvcfFiltering
FilterGVCFSingleFilePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
filterHaplotypeGraph(HaplotypeGraph) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs: This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
filterHaplotypeGraph(HaplotypeGraph, List<Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs: This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
filterRefRanges() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: Name of ref range filter file
filterRefRanges(String) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: Set Filter Ref Range File.
finalSnpFiltering(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
findAlignmentsToReturn(List<String>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Finds groups of 3 or more lines that have descending start values, and where the position of 1 is no more than .01 percent away from the start of the next value.
findAsmIndelStart(Collection<String>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
FindHaplotypeClustersPlugin - Class in net.maizegenetics.pangenome.hapcollapse: Processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed in future steps into a consensus haplotype.
FindHaplotypeClustersPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
FindHaplotypeClustersPlugin.CLUSTER_METHOD - Enum in net.maizegenetics.pangenome.hapcollapse
FindProteomeGenesInAssembly - Class in net.maizegenetics.pangenome.pipelineTests: NOTE: Needs to be re-worked with new db.
FindProteomeGenesInAssembly() - Constructor for class net.maizegenetics.pangenome.pipelineTests.FindProteomeGenesInAssembly
FindRampSeqContigsInAssemblies - Class in net.maizegenetics.pangenome.processAssemblyGenomes: This method takes a fasta of ramp seq short sequences, and looks for them in an assembly genome.
FindRampSeqContigsInAssemblies() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
findRefIndelStart(int, Collection<String>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Find the lowest reference start entry from a mummer snp file list of entries.
FindTrimmedAnchorCoordinates - Class in net.maizegenetics.pangenome.db_loading: NOTE: This version works on the REF only.
FindTrimmedAnchorCoordinates() - Constructor for class net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
FindTrimmedAssemblyCoordinates - Class in net.maizegenetics.pangenome.db_loading: THis file is similar to FindTrimmedAnchorCoordinates used for the reference.
FindTrimmedAssemblyCoordinates() - Constructor for class net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
findVCListForAnchor(List<VariantContext>, int, int) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Find a subset of the VariantContext.
firstReferenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns the first reference range in this graph.
firstReferenceRange(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns the first reference range for the given chromosome.
freqChartHaplotypeCollapse(String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
freqHaplotypeCollapse(String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
fullRefCoordinateToChromCoordinate(ArrayList<Long>) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

G

geneCoordinates() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
geneEnd() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
geneFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Tab delimited .txt file containing gene-only GFF data from reference GFF file,
geneFile(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Set Gene File.
GeneGFFData - Class in net.maizegenetics.pangenome.db_loading
GeneGFFData(int, int, String) - Constructor for class net.maizegenetics.pangenome.db_loading.GeneGFFData
GenerateHaplotypeCallerScripts - Class in net.maizegenetics.pangenome
GenerateHaplotypeCallerScripts() - Constructor for class net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
generateMetrics(Multiset<HaplotypeNode>, Multiset<HaplotypeNode>) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
geneStart() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
GenoHaploData - Class in net.maizegenetics.pangenome.db_loading: Object to hold data needed to populate the genotypes and haplotypes tables.
GenoHaploData(int, boolean, String, String, boolean, boolean, int, float) - Constructor for class net.maizegenetics.pangenome.db_loading.GenoHaploData
genomeData() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Path to tab-delimited file containing genome speciic data with header line: Genotype Hapnumber Dataline Ploidy Reference GenePhased ChromPhased Confidence Method MethodDetails RefVersion
genomeData(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Set Genome Data File.
genomeData() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: Path to tab-delimited file containing genome speciic data with header line: Genotype Hapnumber Dataline Ploidy Reference GenePhased ChromPhased Confidence Method MethodDetails RefVersion
genomeData(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: Set Genome Data File.
genomeFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Input assembly genome file from which to pull sequence
genomeFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Set Assembly Genome.
genomeSequence(long, long) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genomeSequence(long, long) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeSequenceAsString(long, long) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genomeSequenceAsString(long, long) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeSize() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genomeVersionName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
genotype(Chromosome, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotype(Chromosome, Position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotype(Chromosome, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotype(Chromosome, Position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotype(Position) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
genotype(int, int) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
genotypeAsString(Chromosome, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome, Position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome, int, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
genotypeAsString(Chromosome, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeAsString(Chromosome, Position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
genotypeAsString(Chromosome, int, int) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
getAdjustedMummerCoordEntry(String, int) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
getAlternate() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getAnchorFromIntervalsFile(String, String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getAnchorRangeSet(Map<Integer, ReferenceRange>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Create a RangeSet from a map of ranges
getAnchorRangeSet(RangeMap<Integer, String>) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getButtonName() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getChromNamesForHaplotype(String, int, String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Method grabs a list of distinct chromosome names for a genome_interval version
getChromNamesForHaplotype(String, int, String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getChromosome() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getCoordsEntriesForAnchor(Range<Integer>, RangeMap<Integer, String>) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getCoordsRangeMap(List<String>, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Create range map from list of entries from a Mummer coordinates file
getDataFromAssembly(String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
GetDBConnectionPlugin - Class in net.maizegenetics.pangenome.db_loading: Plugin takes a configFile with db specifics and a boolean indicating whether a new db shoudl be created.
GetDBConnectionPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
GetDBConnectionPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
GetDBConnectionPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getEnd() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getEntryFromTabDelimitedLine(String, int, int) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Returns the value for a specific column in a tab-delimited string
GetFastaSequenceLengths - Class in net.maizegenetics.pangenome: Created by terry on 3/19/17.
GetFastaSequenceLengths() - Constructor for class net.maizegenetics.pangenome.GetFastaSequenceLengths
getGameteGroupIDFromTaxaList(List<String>) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Takes a list of taxa and returns the corresponding gamete_group_id or 0
getGameteGroupIDFromTaxaList(List<String>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getGenoidFromLine(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Return genoid
getGenoidFromLine(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getGenomeSequenceValues() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
getGenotypeString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getHapCountsIDAndDataForVersionMethod(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
getHapCountsIDAndDataForVersionMethod(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHapCountsIDAndPathsForMethod(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
getHapCountsIDAndPathsForMethod(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHapidForGenoidHapNumber(int, int) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns hapid for given line name and hap_number
getHapidForGenoidHapNumber(int, int) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHapidHapNumberLineNamesForLines(List<String>) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Retrieves line name and hapnumber, and returns them with the hapid.
getHapidHapNumberLineNamesForLines(List<String>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHapidMapFromLinenameHapNumber() - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns a map of created from the genotypes and haplotypes table.
getHapidMapFromLinenameHapNumber() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHapidsForGenoid(int) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns list of hapids for a given line name
getHapidsForGenoid(int) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getHaplotypeIDFromFastaIDLine(String, String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
getHaplotypeIDFromFastaIDLine(String, String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getIcon() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
getIcon() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getIcon() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
getIcon() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getIcon() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getIndelRanges(RangeMap<Position, List<Position>>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
getInstance(String, ReferenceRange, double, String) - Static method in class net.maizegenetics.pangenome.api.HaplotypeSequence: Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of the original mutable object
getInstanceFromHapidCountMap(TreeMap<ReferenceRange, List<HaplotypeNode>>, Map<Integer, Integer>, double) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getInstanceFromHapidCounts(TreeMap<ReferenceRange, List<HaplotypeNode>>, Multiset<Integer>, double) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getInstanceFromNodeCounts(TreeMap<ReferenceRange, List<HaplotypeNode>>, Multiset<HaplotypeNode>, double) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getIntervalRangesWithIDForChrom(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns sorted treeRangeMap of Positions for specified chromosome
getIntervalRangesWithIDForChrom(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getLineNameHapNumberFromHapid(int) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Method to retrieve both a line name and the hap number given a hapid.
getLineNameHapNumberFromHapid(int) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getMapFromFasta(String) - Static method in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence: Load a fasta file in a map, headers are keys and sequences are values assumes a fasta file in which sequences are not breaked between lines
getMapFromFasta(String) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
getMeanDepth(String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to compute the mean of the depths.
getMeanDepth(String, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getMedianDepth(String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to calculate the Median depth for a GVCF file.
getMedianDepth(String, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getMethodIdFromName(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns method_id given a method name.
getMethodIdFromName(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getModeDepth(String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation: Simple method to get the mode of the depth.
getModeDepth(String, String) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
getNumAlignedBases(RangeSet<Integer>) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getNumberOfStates() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
getProbObsGivenState(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getProbObsGivenState(int, int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
getRangesForChrom(Map<Integer, ReferenceRange>, Chromosome, DBLoadingUtils.AnchorType) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getRangesForChrom(Map<Integer, ReferenceRange>, Chromosome, DBLoadingUtils.AnchorType) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getReference() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getRefLineName(Connection) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Returns the line name of the reference genotype
getRefRangeIDFromString(String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData: Returns reference range id
getRefRangeIDFromString(String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
getRegionCoverage(RangeSet<Integer>, Range<Integer>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: This method takes a RangeSet of integers, and a single range.
getRegionCoverage(RangeSet<Integer>, Range<Integer>) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getStart() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
getStartEndCoordinates(String, boolean) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Find the start/end coordinates from a tab-delmimited Mummer4 coords file entry
getSubMap(Range<Tuple<Integer, Integer>>) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
getToolTipText() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
getTransitionProbability(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
getVariantContextFromHaplotypeNodeList(List<HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils: Method to extract the VCF VariantContexts from a List of HaplotypeNodes
getVariantContextFromHaplotypePath(HaplotypePath) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils: Method to extract the VCF VariantContexts from the HaplotypePath.
graphExportBasename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The base name for R-igraph export files.
graphExportBasename(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Graph Export.
GraphIO - Class in net.maizegenetics.pangenome.api
GraphUtils - Class in net.maizegenetics.pangenome.api
gvcf() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
gvcf() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: GVCF file used to create the haplotype fasta file
gvcf(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin: Set GVCF File.
GVCFGenotypeSequence - Class in net.maizegenetics.pangenome.fastaExtraction: GVCFGenotypeSequence This class should be used instead of GVCFSequence when you want to have diploid calls being returned.
gVCFInputDir() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Directory holding the GVCF files to be filtered.
gVCFInputDir(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Gvcf Dir.
gVCFOutputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Directory for gvcf files to be output for later use
gVCFOutputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set GVCF Output Dir.
GVCFSequence - Class in net.maizegenetics.pangenome.fastaExtraction: GVCFSequence.java
GVCFSequence() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
GVCFStats - Class in net.maizegenetics.pangenome
GVCFStats() - Constructor for class net.maizegenetics.pangenome.GVCFStats
GVCFTyperPlugin - Class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 8/1/17.
GVCFTyperPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
GVCFTyperPlugin.EMIT_MODE - Enum in net.maizegenetics.pangenome.hapcollapse
GVCFUtils - Class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 9/6/17.
GVCFUtils() - Constructor for class net.maizegenetics.pangenome.hapcollapse.GVCFUtils

H

HapCallingUtils - Class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 8/29/17.
HapCallingUtils() - Constructor for class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
HapCountBestPathPlugin - Class in net.maizegenetics.pangenome.hapCalling
HapCountBestPathPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
HapCountBestPathToTextPlugin - Class in net.maizegenetics.pangenome.hapCalling: This plugin processes haplotype node data either from of an inclusion file, or from PHG database tables.
HapCountBestPathToTextPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
hapCountMethod() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Method name used to create haplotype counts, as stored in db table methods
hapCountMethod(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Set Hap Count Method.
hapCountMethod() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Name of method used to creates inclusion/exclusion counts in FastqToHapCountPLugin
hapCountMethod(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Hap Count Method.
hapidCountFilename - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
hapidCountMap() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
hapidCountMap(Map<Integer, Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
hapidCountMapFileName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
hapidCounts(Multiset<Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
hapidExclusionCountMap(Map<Integer, Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
hapids() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: List of haplotype ids to include in the graph.
hapids(SortedSet<Integer>) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Haplotype Ids.
haplotypeCountsId() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: DB assigned haplotype_counts_id from the haplotype_counts table.
haplotypeCountsId(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Hap Counts Id.
haplotypeCountsToPath() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
haplotypeCountsToPathProbability() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
HaplotypeEdge - Class in net.maizegenetics.pangenome.api
HaplotypeEdge(HaplotypeNode, HaplotypeNode, double) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeEdge: Constructor
HaplotypeGraph - Class in net.maizegenetics.pangenome.api: This Class is a wrapper around a complete Practical Haplotype Graph (PHG).
HaplotypeGraph(Collection<HaplotypeEdge>) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeGraph: Constructor for HaplotypeGraph.
HaplotypeGraphBuilderPlugin - Class in net.maizegenetics.pangenome.api
HaplotypeGraphBuilderPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
HaplotypeNode - Class in net.maizegenetics.pangenome.api
HaplotypeNode(HaplotypeSequence, TaxaList, int, byte[]) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeNode
HaplotypeNode(HaplotypeSequence, TaxaList, int) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeNode
HaplotypeNode(HaplotypeSequence, TaxaList) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeNode
HaplotypeNode.VariantInfo - Class in net.maizegenetics.pangenome.api: These are instantiated only when requested.
HaplotypePath - Class in net.maizegenetics.pangenome.api: Created on June 20, 2017
haplotypeSequence() - Method in class 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
haplotypesGenomeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Fasta file and associated BWA indices for haplotypes
haplotypesGenomeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Haplotype File.
haplotypesGenomeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Fasta file and associated BWA indices for haplotypes
haplotypesGenomeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Haplotype File.
hapNumber() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
hashCode() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
hashCode() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
hostname() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Hostname where database resides
hostname(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Hostname.
hostname() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Hostname where database resides
hostname(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Set Hostname.
hostname() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Hostname where database resides
hostname(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Hostname.
howManyAnchorsHaveW22InMostFrequentNode(HaplotypeGraph, Multiset<Integer>) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils

I

id() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
id() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: Identifier for a unique reference range
ImportHaplotypePathFilePlugin - Class in net.maizegenetics.pangenome.hapCalling: Plugin to import the haplotypePath files produced by ExportHaplotypePathToFilePlugin.
ImportHaplotypePathFilePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
includeAnchors() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Whether to include anchors
includeAnchors(Boolean) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Set Include Anchors.
includeInnerAnchors() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Whether to include inner anchors
includeInnerAnchors(Boolean) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Set Include Inner Anchors.
includeVariantContexts() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Whether to include variant contexts in haplotype nodes.
includeVariantContexts(Boolean) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Include Variant Contexts.
inclusionCountMap(Map<Integer, Integer>) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
inclusionFilename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The name of the file containing read inclusion and exclusion counts for hapids.
inclusionFilename(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Inclusion File.
inclusionFilenameDir() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: The name of the file containing read inclusion and exclusion counts for hapids.
inclusionFilenameDir(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Inclusion File Dir.
inclusionFilenameDir() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: The name of the file containing read inclusion and exclusion counts for hapids.
inclusionFilenameDir(String) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: Set Inclusion File Dir.
IndexHaplotypeKmersPlugin - Class in net.maizegenetics.pangenome.hapCalling: author edbuckler
IndexHaplotypeKmersPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
INNER_ANCHOR_METHOD - Static variable in class net.maizegenetics.pangenome.api.CreateGraphUtils
input() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin: Input VCF file
input(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin: Set Input.
inputFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Input fasta file with consensus sequences
inputFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Set Input File.
inputFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: GVCF File to be filtered.
inputFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Set Input G V C F File.
inputFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: GVCF File to be filtered.
inputFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Set Input G V C F File.
inputFileDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin: Input file directory
inputFileDirectory(String) - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin: Set Input File Directory.
inputGVCFDir() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Input gvcf directory.
inputGVCFDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Input GVCF Directory.
inputIntervalFile() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Input interval file to run GVCFTyper with.
inputIntervalFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Input Interval File.
inReferenceRange(Position) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
inReferenceRange(int, int) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
instance(String, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Returns an initialized GVCFSequence given the input Reference and GVCF Files.
instance(GenomeSequence, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Returns an initialized GVCFSequence given the input Reference and GVCF Files.
instance(GenomeSequence, String, boolean) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Instance method to allow for reference filling in missing for a file
instance(GenomeSequence, List<VariantContext>, boolean, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Instance method to build the GenomeSequence in memory using a List of VariantContexts
instance(String, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence: Returns an initialized GVCFSequence given the input Reference and GVCF Files.
instance(GenomeSequence, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence: Returns an initialized GVCFSequence given the input Reference and GVCF Files.
instance(GenomeSequence, String, boolean) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence: Instance method to add in missing as Ref from a file
instance(GenomeSequence, List<VariantContext>, boolean, String) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence: Instance method to create a GenomeSequenc from a List of VariantContexts
intervalCoordinates() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
intervalFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin: Intervals file
intervalFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin: Set Intervals.
intervalFile() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Interval File used to create the VCF file
intervalFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Interval File.
intervalsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Anchor Intervals file to be used when intervals are different than DB, e.g.
intervalsFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Anchor Intervals File.
intervalString() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
is_reference() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
isAltSeqSameAsRefExcludingNs(String, String) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
isAnchor() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: Return whether this range is an anchor.
isAnchor() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
isGca() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: GCA fastas have long text as idLines.
isGca(Boolean) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Set Is GCA.
isHet() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
isPerfectMatch(SAMRecord) - Static method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
isPhasedAcrossChromosomes() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
isPhasedAcrossGenes() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
isRefBlock(VariantContext) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: Simple method to check to see if the Variant is a reference block
isRefBlock(VariantContext) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Simple method to determine if the current variant context is a reference block or not.
isVariant() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo

K

keepRefRanges(HaplotypeGraph, List<ReferenceRange>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Creates graph that includes specified reference ranges.

L

lastReferenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns the last reference range in this graph.
lastReferenceRange(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns the last reference range for the given chromosome.
leftEdges(HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns List of Left HaplotypeEdges for given HaplotypeNode
leftHapNode() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge: HaplotypeNode to the left of the current edge.
leftTrimCount() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
likelihood() - Method in class net.maizegenetics.pangenome.api.HaplotypePath: Likelihood of haplotype path calculated from all included haplotype nodes
line_data() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
line_name() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
listBadNodes(String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
listTaxa() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs: Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.out
listTaxa(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
listTaxaForPHG() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
loadAssemblyDataToDB(int, String, Connection, Map<Integer, AnchorDataPHG>) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Load the assembly haplotype data to the database
LoadConsensusAnchorSequencesPlugin - Class in net.maizegenetics.pangenome.db_loading: This method takes an input file in fasta format and adds the sequences to the data base.
LoadConsensusAnchorSequencesPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
LoadConsensusAnchorSequencesPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
LoadConsensusAnchorSequencesPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
loadDataFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: File holding the DB config information
loadDataFile(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Set Load Data File.
loadDb() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Whether to populate the haplotype_counts table - often false when testing
loadDb(Boolean) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set LoadDb.
LoadGenomeIntervalsToPHGdbPlugin - Class in net.maizegenetics.pangenome.db_loading: Before running this plugin, GetDBConnectionPlugin must be run.
LoadGenomeIntervalsToPHGdbPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
LoadGenomeIntervalsToPHGdbPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
LoadGenomeIntervalsToPHGdbPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
LoadHaplotypeCountsTablePlugin - Class in net.maizegenetics.pangenome.db_loading: This method reads haplotype counts from an incoming DataSet object, and stores results to a specified database.
LoadHaplotypeCountsTablePlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
LoadHaplotypeCountsTablePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
LoadHapSequencesFromGVCFPlugin - Class in net.maizegenetics.pangenome.db_loading: Plugin which will upload a GVCF file to the DB.
LoadHapSequencesFromGVCFPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
LoadHapSequencesToDBPlugin - Class in net.maizegenetics.pangenome.db_loading: This method takes data processed through GATK haplotype caller, or through processAssebmlyGenomes.Minimap2PipelinePlugin.
LoadHapSequencesToDBPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
LoadHapSequencesToDBPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
LoadHapSequencesToDBPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
loadInitialAssemblyData(String, String, Connection) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: load initial genotype and method data to the database
localConsensusDirectoryOut - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
localDirectoryOut - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
lowerPoissonBound() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Lower Poisson Bound used for filtering.
lowerPoissonBound(Double) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Lower Poisson Bound.

M

main(String[]) - Static method in class net.maizegenetics.pangenome.CompareFastaToReference
main(String[]) - Static method in class net.maizegenetics.pangenome.CompareHaplotypesToAssembly
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
main(String[]) - Static method in class net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
main(String[]) - Static method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
main(String[]) - Static method in class net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU
main(String[]) - Static method in class net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
main(String[]) - Static method in class net.maizegenetics.pangenome.GetFastaSequenceLengths
main(String[]) - Static method in class net.maizegenetics.pangenome.GVCFStats
main(String[]) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
main(String[]) - Static method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
main(String[]) - Static method in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
main(String[]) - Static method in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
main(String[]) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
main(String[]) - Static method in class net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper
main(String[]) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
main(String[]) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
main(String[]) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
main(String[]) - Static method in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
main(String[]) - Static method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
main(String[]) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
main(String[]) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
main(String[]) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
main(String[]) - Static method in class net.maizegenetics.pangenome.Utils.CreateHashForFiles
mainProcessDataJustGenes(String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
mainProcessMergeOverlapsAddGapDifference(String, String, String, int) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
maxDistFromFounder() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Maximum genetic divergence from founder haplotype to cluster sequences
maxDistFromFounder(Double) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Max divergence from founder.
maxError() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Maximum error allowed to create a homozygous call.
maxError(Double) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Maximum error.
maxNodesPerRange(int) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
maxNodesPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: maximum number of nodes per reference range.
maxNodesPerRange(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Max Nodes.
maxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: maximum number of include counts per anchor reference range.
maxReadsPerKB(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Max Reads.
maxReadsPerRangeKB(int) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
maxTaxaPerRange(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
mergeCoords(String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Deprecated.
MergeGVCFPlugin - Class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 11/6/17.
MergeGVCFPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
MergeGVCFUtils - Class in net.maizegenetics.pangenome.hapcollapse: Created by zrm22 on 11/7/17.
MergeGVCFUtils() - Constructor for class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
mergeRule() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: The rule in which to resolve the conflicting Indels after consensus has been found.
mergeRule(FillIndelsIntoConsensus.INDEL_MERGE_RULE) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Indel Merge Rule.
method() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Consensus Method
method(String) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Consensus Method.
method(ReferenceRangeEmissionProbability.METHOD) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
method() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Name of method used for determining inclusion/exclusion counts
method(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Set Hapcount Method.
method() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Name of method used when creating the haplotypes to be pulled
method(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Method.
method() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Name of method used to create hap counts, for the haplotype_counts table.
method(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Method.
method() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Consensus Method
method(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Consensus Method.
methodDetails() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Description of methods used to collapse the anchor sequences.
methodDetails(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Set Collapse Method Description.
methodDetails() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Text describing method used to create inclusion/exclusion counts.
methodDetails(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin: Set Method Details.
methodId(Connection, String) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Returns method id (methods.method_id) for given method name.
methodIdName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
minCountTaxa() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Minimun number of taxa represented in reference range for reference range to remain in graph
minCountTaxa(Integer) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Set Min Count Taxa.
minPercentTaxa() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Minimum percent of taxa represented in reference range for reference range to remain in graph.
minPercentTaxa(Double) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Set Min Percent Taxa.
minProbBF() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
minReads() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: minimum number of reads per anchor reference range.
minReads(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Min Reads.
minReadsPerRange(int) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
minSiteForComp() - Method in class 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) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Min sites to cluster.
minTaxaCoverage() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: The minimum proportion of sites present in a taxa to go into clustering
minTaxaCoverage(Double) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Min taxa coverage.
minTaxaInGroup() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Minimum number of taxa to generate a haplotype
minTaxaInGroup(Integer) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Min taxa to generate a haplotype.
minTaxaPerRange(int) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
minTaxaPerRange - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
minTaxaPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: minimum number of taxa per anchor reference range.
minTaxaPerRange(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Min Taxa.
minTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: minimum probability of a transition between nodes at adjacent reference ranges.
minTransitionProb(Double) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Min Transition Prob.
minTransitionProbability(double) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
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.
Mummer4DoonerBZStats() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
Mummer4DoonerBZStats(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
Mummer4DoonerBZStats(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
mummer4Path() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Path to mummer4 binaries
mummer4Path(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Mummer4 binary path
MummerAnalysisMetricsPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes: This method provides summary statistics on mummer output.
MummerAnalysisMetricsPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
MummerAnalysisMetricsPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
MummerAnalysisMetricsPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
mummerParams() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Mummer parameters used
mummerParams(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Mummer Parameters.
mummerParams() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Parameters used when running mummer
mummerParams(String) - Method in class 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.
MummerScriptProcessing() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

N

name() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
name() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Name to give each file, e.g w22.
name(String) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Set Name .
net.maizegenetics.pangenome - package net.maizegenetics.pangenome
net.maizegenetics.pangenome.api - package net.maizegenetics.pangenome.api
net.maizegenetics.pangenome.db_loading - package net.maizegenetics.pangenome.db_loading
net.maizegenetics.pangenome.fastaExtraction - package net.maizegenetics.pangenome.fastaExtraction
net.maizegenetics.pangenome.gui - package net.maizegenetics.pangenome.gui
net.maizegenetics.pangenome.gvcfFiltering - package net.maizegenetics.pangenome.gvcfFiltering
net.maizegenetics.pangenome.hapCalling - package net.maizegenetics.pangenome.hapCalling
net.maizegenetics.pangenome.hapcollapse - package net.maizegenetics.pangenome.hapcollapse
net.maizegenetics.pangenome.multiSequenceAlignment - package net.maizegenetics.pangenome.multiSequenceAlignment
net.maizegenetics.pangenome.pipelineTests - package net.maizegenetics.pangenome.pipelineTests
net.maizegenetics.pangenome.processAssemblyGenomes - package net.maizegenetics.pangenome.processAssemblyGenomes
net.maizegenetics.pangenome.trimAnchors - package net.maizegenetics.pangenome.trimAnchors
net.maizegenetics.pangenome.Utils - package net.maizegenetics.pangenome.Utils
NO_CONSENSUS_METHOD - Static variable in class net.maizegenetics.pangenome.api.CreateGraphUtils
nodeListFromProbabilities(double, String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
nodeListFromProbabilities(double) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
nodeMap(TreeMap<ReferenceRange, List<HaplotypeNode>>) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
nodes(HaplotypeGraph, SortedSet<Integer>) - Static method in class net.maizegenetics.pangenome.api.GraphUtils: Returns a list of HaplotypeNodes corresponding to the given hapids in the given graph.
nodes(ReferenceRange) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns list of HaplotypeNodes for given ReferenceRange
nodes() - Method in class net.maizegenetics.pangenome.api.HaplotypePath
nodesContainingExactly(TaxaList, HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.GraphUtils: Gets list of HaplotypeNodes containing exact list of taxa.
nodesOnPath() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
nodesSplitByIndividualTaxa(HaplotypeGraph, double) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
nodeStream() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
nodeTaxaPairs(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
numberOfChromosomes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
numberOfChromosomes() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
numberOfLeftEdges(HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Return number of left edges for given node.
numberOfNodes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
numberOfRanges() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns number of reference ranges in this graph.
numberOfRightEdges(HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Return number of right edges for given node.
numberTaxa(ReferenceRange) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns number of taxa represented by given reference range.
numErrorAllowed() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Maximum allowable error in order to count the read mapping
numErrorAllowed(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Allowed Error.
numErrorAllowed() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Maximum allowable error in order to count the read mapping
numErrorAllowed(Integer) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Allowed Error.
numFlanking() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Number of flanking basepairs to add at each end of the gene sequence
numFlanking(Integer) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Set Number of Flanking BPs.
numTaxa() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode: Number of taxa used when consensus sequence was created or one if this is an original sequence.
numThreads() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Number of threads for Sentieon to use.
numThreads(Integer) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Num Threads.

O

old(String[]) - Static method in class net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
onlyAnchors() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Whether to include only anchors (i.e.
onlyAnchors(Boolean) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Only Anchors.
onlyAnchors() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Whether to include only anchors (i.e.
onlyAnchors(Boolean) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Only Anchors.
onlyGenic() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: True means create vcf only for hte genic intervals.
onlyGenic(Boolean) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Only Genic.
outFile() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Output file directory name, or new directory path; Directory will be created, if doesn't exist.
outFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Donor dir/file basename.
output() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: File Name of the filtered read output
output(String) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: Set Output File.
outputAllSNPs() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Whether to output all SNPs known by haplotype graph.
outputAllSNPs(Boolean) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Set Output All SNPs.
outputBase() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: base name for output files from this Plugin.
outputBase(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Output file base.
outputDir() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Directory where output files will be written
outputDir(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Set Output Directory.
outputDir() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Path to write the split files
outputDir(String) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin: Set Output Directory.
outputDir() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Directory to hold the output files.
outputDir(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Output Dir.
outputDir() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Output Directory
outputDir(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Output Dir.
outputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Directory where you want to store the output VCFs
outputDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Set Output Dir.
outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Output directory including trailing / for writing files
outputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Output Directory.
outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Output fastq file to use as input for BWA-MEM
outputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin: Set Output File.
outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Output directory including trailing / for writing files
outputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Output Directory.
outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Output directory including trailing / for writing files
outputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Output Directory.
outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Output Directory
outputDir(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Output Directory.
outputFile() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Output filename
outputFile(String) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin: Set Output File.
outputFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Output GVCF File Path and Name.
outputFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Set Output G V C F File.
outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: FUll path to output file created by this plugin .
outputFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Output File.
outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Output file name
outputFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Set Output File.
outputFile() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Output File
outputFile(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Output File.
outputFile() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Output File
outputFile(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Set Output File.
outputFileDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Output file directory
outputFileDirectory(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Set Output File Directory.
outputFileName() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: Name of output file
outputFileName(String) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin: Set Output File.
outputVCFDir() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Output VCF file directory.
outputVCFDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Output VCF Directory.

P

parseCoordinateRegions(String, String) - Static method in class 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.
parseGCA(String) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
parseMummerSNPFile(String, String) - Static method in class 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
password() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Password for database
password(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Password.
password() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Password for database
password(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Set Password.
password() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Password for database
password(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Password.
path(TreeMap<Chromosome, HaplotypePath>) - Static method in class net.maizegenetics.pangenome.api.GraphUtils: Returns sorted set of haplotype ids from the given paths.
path(String, List<HaplotypeNode>) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome given the specified taxon and list of known HaplotypeNodes.
path(Taxon, List<HaplotypeNode>) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome given the specified Taxon and list of known HaplotypeNodes.
path(List<HaplotypeNode>) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome given the specified list of known HaplotypeNodes.
path(String) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome given the specified taxon.
path(Taxon) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome given the specified Taxon.
path() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns most probable HaplotypePath for each Chromosome.
pathInfoFilename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The name of the file to which detailed path diagnostic information will be written.
pathInfoFilename(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Path Info File.
pathMethod() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Name of method used to create paths, as it should appear in the paths table
pathMethod(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Set Path Method.
pathMethod() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Name of method to be used to create paths through the graph.
pathMethod(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set P Method.
pathMethodDetails() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Description of method used to create paths - optional
pathMethodDetails(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Set Path Method Details.
pathName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The path method name assigned when the path was created and stored in the DB.
pathName(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Path method name.
pathsDir() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin: Paths directory
pathsDir(String) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin: Set Paths Directory.
pathsToNodes(TreeMap<Chromosome, HaplotypePath>) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
PathsToVCFPlugin - Class in net.maizegenetics.pangenome.hapCalling
PathsToVCFPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
PathToIgraphPlugin - Class in net.maizegenetics.pangenome.hapCalling
PathToIgraphPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
phasingConfidence() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
PHGData - Interface in net.maizegenetics.pangenome.db_loading
PHGDataWriter - Interface in net.maizegenetics.pangenome.db_loading
PHGdbAccess - Class in net.maizegenetics.pangenome.db_loading: Access methods for postgres or SQL PHG dbs.
PHGdbAccess(Connection) - Constructor for class net.maizegenetics.pangenome.db_loading.PHGdbAccess
ploidy() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
pluginDescription() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
postProcessParameters() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
postProcessParameters() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
prefix() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Name to prefix to output results file
prefix(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Output File refix.
prefix() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Name to prefix to output results file
prefix(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Output File refix.
presenceAbsenceTaxonByNode(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
printTrimTables(String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
probabilityCorrect(double) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
probabilityOfBeingCorrect(HaplotypeGraph, Multiset<Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
probabilityOfBeingCorrect(Multiset<Integer>, TreeMap<ReferenceRange, List<HaplotypeNode>>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
probabilityOfBeingCorrect(Map<Integer, Integer>, TreeMap<ReferenceRange, List<HaplotypeNode>>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
probabilityReadMappingCorrect(double) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
probReadMappedCorrectly() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: minimum number of reads per anchor reference range.
probReadMappedCorrectly(Double) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Prob Correct.
processCreateHash(String, String) - Static method in class net.maizegenetics.pangenome.Utils.CreateHashForFiles
processData(DataSet) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin: Plugin method to process the data
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
processData(DataSet) - Method in class 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) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
processData(DataSet) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
processData(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
processData(DataSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
processMain(String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
processMain(String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
processMain(String, Map<Integer, String>, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
processMain(String, Map<Integer, String>, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
processMain(String, String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
PurgeSequencesFromAlignments - Class in net.maizegenetics.pangenome.hapcollapse: Created by edbuckler on 6/19/17.
PurgeSequencesFromAlignments() - Constructor for class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
putAllAnchors(List<AnchorDataPHG>, String) - Method in interface 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<AnchorDataPHG>, String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putAssemblyInterAnchorSequences(String, int, String, Multimap<Integer, AnchorDataPHG>) - Method in interface 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<Integer, AnchorDataPHG>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putConsensusSequences(Multimap<Position, Tuple<AnchorDataPHG, List<String>>>, int) - Method in interface 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<Position, Tuple<AnchorDataPHG, List<String>>>, int) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putGameteGroupAndHaplotypes(List<String>) - Method in interface 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<String>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putGenoAndHaploTypeData(GenoHaploData) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: Stores required data to the genotypes and haplotypes tables for each entry on the list.
putGenoAndHaploTypeData(GenoHaploData) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putHaplotypeCountsData(String, String, String, String, byte[]) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: This method adds data to the haplotype_counts table.
putHaplotypeCountsData(String, String, String, String, byte[]) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putHaplotypesForGamete(int, String, Map<Integer, AnchorDataPHG>) - Method in interface 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.
putHaplotypesForGamete(int, String, Map<Integer, AnchorDataPHG>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putHaplotypesForMultipleGroups(Multimap<Position, Tuple<AnchorDataPHG, String>>, int) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: Add data to the haplotypes table.
putHaplotypesForMultipleGroups(Multimap<Position, Tuple<AnchorDataPHG, String>>, int) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putMethod(String, DBLoadingUtils.MethodType, String) - Method in interface 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, String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putPathsData(String, String, Multimap<Integer, HaplotypeNode>) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: This method stores paths data to the paths table.
putPathsData(String, String, Multimap<Integer, HaplotypeNode>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putRefAnchorData(String, int, List<AnchorDataPHG>, String, String, String, String) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: Fills in the haplotypes table for the reference ranges.
putRefAnchorData(String, int, List<AnchorDataPHG>, String, String, String, String) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
putRefRangeRefRangeGroups(int, List<Integer>) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter: Takes a method id and a list of reference ranges.
putRefRangeRefRangeGroups(int, List<Integer>) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess

Q

QualityReportAnchorsToHaplotypes - Class in net.maizegenetics.pangenome.hapcollapse: Created by mm2842 on 6/20/17.
QualityReportAnchorsToHaplotypes() - Constructor for class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
qualityScore() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence: Basis of this score and units to be determined
query() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Name of assembly in mummer query, this is usually the assembly
query(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Query name .

R

RampSeqContigToGenomeIntervalPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes: NOTE: this method created to aid Dan Ilut.
RampSeqContigToGenomeIntervalPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
RampSeqContigToGenomeIntervalPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
RampSeqContigToGenomeIntervalPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
readAnchorIds() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions: Reads in list of anchor region numbers that are IBD
readFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Raw Read file aligned to the reference
readFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Raw Read File.
readFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Raw Read file aligned to the reference
readFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Raw Read File.
readFileName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
readHapidCounts(String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
readHapidMap(String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
reads() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: File Name of the read fastq
reads(String) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: Set Read File.
RedirectStreams - Class in net.maizegenetics.pangenome.processAssemblyGenomes: This comes from https://stackoverflow.com/questions/35706921/redirecting-the-output-of-a-process-into-the-input-of-another-process-using-proc/35709166 It is used to aid in piping output from 1 ProcessBuilder command to another.
RedirectStreams(Process, Process) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RedirectStreams
ref() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Input reference fasta file for single chromosome
ref(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Reference Fasta File.
ref() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Reference fasta File
ref(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Set Reference.
refChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Name of reference chromsome as stored in the database.
refChrom(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Reference Chromosome Name.
reference() - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Input Reference Fasta
reference(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin: Set Ref.
reference() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: File Name of the reference fasta
reference(String) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin: Set Ref File.
reference() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Input Reference Fasta
reference(String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Ref.
reference(Position) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
reference(int, int) - Method in class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
referenceFile() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Input Reference used to create the gvcf
referenceFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin: Set Reference Fasta Sequence.
referenceFile() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Reference Input file
referenceFile(String) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin: Set Reference File.
referenceFileName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Reference file name in case you want to index on the fly
referenceFileName(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Ref File Name.
referenceName() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: Reference genome (B73, CML247, EP1, etc) from which the reference range originates
referenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode: Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details associated with that range of values.
referenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence: Reference Range in (alternative)reference genome
ReferenceRange - Class in net.maizegenetics.pangenome.api
ReferenceRange(String, Chromosome, int, int, int) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRange
ReferenceRange(String, Chromosome, int, int, int, boolean) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRange
ReferenceRangeEmissionProbability - Class in net.maizegenetics.pangenome.api
ReferenceRangeEmissionProbability.Builder - Class in net.maizegenetics.pangenome.api
ReferenceRangeEmissionProbability.METHOD - Enum in net.maizegenetics.pangenome.api
referenceRangeForChromMap(Connection, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Find all reference ranges for a particular chromosome
referenceRangeList() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns list of reference ranges for whole graph.
referenceRangeMap(Connection) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Retrieves all ReferenceRange instances
referenceRanges(Connection) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Retrieves all ReferenceRange instances with specified genome interval version name.
referenceRanges() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns sorted set of reference ranges for whole graph.
referenceRangeStream() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns stream of reference ranges for entire graph.
referenceRangeStream(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns stream of reference ranges for given chromosome.
ReferenceRangeTransitionProbability - Class in net.maizegenetics.pangenome.api
ReferenceRangeTransitionProbability(ArrayList<List<HaplotypeNode>>, HaplotypeGraph, double) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
referenceSequence() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Reference Genome Sequence to use to extract the fasta
referenceSequence(GenomeSequence) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Reference Genome Sequence.
refFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Input reference fasta file
refFasta(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Reference Fasta File.
refFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Fasta file containing reference genome
refFile(String) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Set Ref Genome File.
refFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Reference File used to create the GVCFs.
refFile(String) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Ref File.
refGenome() - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Referemce Genome File for aligning against
refGenome(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin: Set Reference Genome File.
refGenomeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Fasta file and associated BWA indices for haplotypes
refGenomeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Haplotype File.
refGenomeFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Reference genome file - temporary need until we can back convert coordinates
refGenomeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin: Set Ref File.
refilterCoordsFile(String, String, String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: This method post-processes the filtered and original coords file.
refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The name of the file containing the reference ranges to keep.
refRangeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Ref Range File.
refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: The name of the file containing the reference ranges to keep.
refRangeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Ref Range File.
refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The name of the file containing the reference ranges to keep.
refRangeFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Ref Range File.
refRangeForSNPFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Reference Range file used to further subset the paths for only specified regions of the genome.
refRangeForSNPFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: Set Ref Range File V C F.
refRanges() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Reference range list to remove from graph
refRanges(List<ReferenceRange>) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Set Reference Ranges.
refRangesForChrom(Connection, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
refRangesForChrom(Connection, String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
refVersion() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Name of reference version as stored in the DB table genome_inteval_versions
refVersion(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin: Set Ref Version.
removeHaplotypeCaller(String) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: Simple method to remove the _Haplotype_Caller from the taxon name
removeIndels(GenotypeTable) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: Method to Remove indels from the GenotypeTable.
removeLongNs(String) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
RemoveLongRunNs - Class in net.maizegenetics.pangenome.multiSequenceAlignment: Simple test utility(script) which will remove Ns from a list of files TODO Refractor out the methods to be more object oriented Created by zrm22 on 6/7/17.
RemoveLongRunNs() - Constructor for class net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
removeRefRanges(HaplotypeGraph, double) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Removes reference ranges from given graph that represent less than given minimum percent of total taxa.
removeRefRanges(HaplotypeGraph, int) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Removes reference ranges from given graph that represent less than given minimum number of taxa.
removeRefRanges(HaplotypeGraph, List<ReferenceRange>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Removes specified reference ranges from graph.
replaceNsWithMajor() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Boolean flag to replace any N calls with a Major Homozygous Diploid Value
replaceNsWithMajor(Boolean) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Replace N calls with Major Allele.
reportFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
resizeCoords(String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Test method to resize the coordinate files so they are not overlapping
resizeRefBlock(VariantContext, GenomeSequence, Position, boolean) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method which will take a variant Context which needs to be split and will output 2 new variants while updating ASM_* annotations.
ResizeRefBlockPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
ResizeRefBlockPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
ResizeRefBlockPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
resultsfile - Static variable in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
resultsfile - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
rightEdges(HaplotypeNode) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns List of Right HaplotypeEdges for given HaplotypeNode
rightHapNode() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge: HaplotypeNode to the right of the current edge
rightTrimCount() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
run() - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
run(String, String, String) - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs: Setup the run of the tool and start it exporting files.
run(String, String, String) - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
run2() - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
runCollapsePipeline(HaplotypeGraph, String) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: This method will loop through each reference range in the graph and will: 1.
runDeltaFilter(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Call mummer4 delta-filter method with parameter: -g 1-to-1 global alignment not allowing rearrangements NOTE: the -g option filters out many alignments, including inversions.
RunGVCFTyper - Class in net.maizegenetics.pangenome.hapcollapse: Simple class to run the GVCFTyperPlugin until it gets integrated into TASSEL proper.
RunGVCFTyper() - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper
RunHapCollapsePipelinePlugin - Class in net.maizegenetics.pangenome.hapcollapse: Simple plugin to run the full Haplotype Collapse plugin.
RunHapCollapsePipelinePlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
runPlugin(DataSet) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin: Convenience method to run plugin with one return object.
runPlugin(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Convenience method to run plugin with one return object.
runPlugin(DataSet) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Convenience method to run plugin that returns nothing.
runShowCoords(String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: call mummer4 show-coords method
runShowSNPs(String, String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: This method calls show-snps using only a delta file as input
runShowSNPsWithCat(String, String, String, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Fun the mummer4 show-snps entry against a delta file, using a coords file as additional input.

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samFileName - Static variable in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
ScoreRangesByInclusionCountsPlugin - Class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 10/11/17.
ScoreRangesByInclusionCountsPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
searchSeqsInFasta(Map<String, String>, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
seqErrorRate() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Error rate used to merge alleles call hets versus homozygous
seqErrorRate(Double) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Sequencing error rate.
seqHash() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence: Sequence hash in md5
seqHash() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
seqLen() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
sequence() - Method in class net.maizegenetics.pangenome.api.HaplotypePath: Sequence from nodes comprising this path.
sequence() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence: String representation of this nucleotide sequence
sequence() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
sequenceOutDir() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Output Directory For storing the sequence files
sequenceOutDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Sequence Output Directory.
setNode(int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
setUp() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
setUp() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
setUpClass() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
setUpClass() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
setUpClass() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFWithIBDTest
setupIndelVariants(Map<Range<Position>, List<Position>>, GenomeSequence, GenomeSequence) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method to fill in the unmapped regions coming from nucmer.
ShellScript_createLoadHaplotypes - Class in net.maizegenetics.pangenome.db_loading: Takes a list of fasta file, creates a chell script to load them.
ShellScript_createLoadHaplotypes() - Constructor for class net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
showNodeCounts() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs: Diagnostic method that writes the HaplotypeNode counts of the first 20 ranges to System.out
SimpleGVCFReader - Class in net.maizegenetics.pangenome.pipelineTests: Created by edbuckler on 6/22/17.
SimpleGVCFReader(String, String, int, int) - Constructor for class net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
snpPositions(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.GraphUtils: Return sorted set of positions that are variant (SNP) positions in given graph.
snpPositions(HaplotypeGraph, Collection<Integer>) - Static method in class net.maizegenetics.pangenome.api.GraphUtils: Return sorted set of positions that are variant (SNP) positions in given graph.
sortListCreatehash() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
splitCigar(String) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
SplitFastaByChromPlugin - Class in net.maizegenetics.pangenome.db_loading: Splits fasta by chromosome.
SplitFastaByChromPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
SplitFastaByChromPlugin(Frame) - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
SplitFastaByChromPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
SplitMafftRun - Class in net.maizegenetics.pangenome.multiSequenceAlignment: Simple utility to create a multithreaded script to run multiple anchors through MAFFT at a single time.
SplitMafftRun() - Constructor for class net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
splitOverlappingCoordsEntries(List<String>, List<String>, boolean) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Splits overlapping entries, The mummer4 coords file entries will have these tab-delimited columns: S1 E1 S2 E2 Len1 Len2 %ID refID asmID The files processed were sorted by ref-coordiates via the show-coords -r param, so S1/E1 is ref coords and S2/E2 are the assembly coordinates.
splitRefRange(List<VariantContext>, Map<Integer, ReferenceRange>, GenomeSequence) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method to split up the reference range by anchor mappings.
splitTaxa(boolean) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
splitTaxa() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: split consensus nodes into one node per taxon.
splitTaxa(Boolean) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Split Taxa.
splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon.
splitTransitionProb(Double) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Split Prob.
splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon.
splitTransitionProb(Double) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Split Prob.
SplitVCFIntoIntervalsPlugin - Class in net.maizegenetics.pangenome.gvcfFiltering
SplitVCFIntoIntervalsPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
splitW22GenomeGetChrom10() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
start() - Method in class net.maizegenetics.pangenome.api.ReferenceRange: Start position of reference range, inclusive
start() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
startNodes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns list of HaplotypeNodes that start graph.
startNodes(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
startProbabilities(List<HaplotypeNode>) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
storeFastqToHapCountResult() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
storeHapidCounts(String, Multiset<Integer>) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
storeHapidMap(String, Map<Integer, Integer>) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
subsetGraph(HaplotypeGraph, TaxaList) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Create graph that's a subset of the given graph which contains only nodes from the taxa list.

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tagCountsByTaxaFile() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin: File holding the tag counts for each taxa
tagCountsByTaxaFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin: Set Tag Count By Taxa File.
tagNodePairCounts(String, HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
tagToHapIdMapFile() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin: tagToHapIDMappingFile
tagToHapIdMapFile(String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin: Set Hap Id Mapping File.
target() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Name of target in mummer query, this is usually the reference
target(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Target name.
targetTaxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
targetTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: The taxon that will be used to evaluate the node list returned.
targetTaxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Target.
targetTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: The taxon that will be used to evaluate the node list returned.
targetTaxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Target.
taxaFilter(TaxaList) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Taxa.
taxaFilterList(String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
taxaFilterList(TaxaList) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: A comma delimited list of taxa (no spaces allowed) to include in graph.
taxaFilterString(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Taxa.
taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: A comma delimited list of taxa (no spaces allowed) to include in graph.
taxaFilterString(String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Taxa.
taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: A list of taxa to include in graph.
taxaInGraph() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Return all taxa represented in this graph.
taxaInNodes(TreeMap<ReferenceRange, List<HaplotypeNode>>) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
taxaInRange(ReferenceRange) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns taxa represented by given reference range.
taxaList() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Optional list of taxa to include.
taxaList(TaxaList) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Set Taxa List.
taxaList(String) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin: Set Taxa List.
taxaList() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode: List of taxa used when the consensus sequence was created or a single taxon.
taxaListMap(Connection) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils: Retrieves all groups of taxa.
taxon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Name of taxon whose variant contexts should be pulled.
taxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Taxon.
taxon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Taxon
taxon(String) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin: Set Taxon.
taxon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Name to be assigned for the taxon
taxon(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Set Taxon Name.
taxonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The name of the taxon for which the path is requested.
taxonName(String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Taxon name.
tearDown() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
tearDown() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
tearDownClass() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
tearDownClass() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
testB73W22() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
testChrMatch() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
testChromLength(String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
testFastqToHapCount(String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
testHapidCounts(HaplotypeGraph, String) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
testIBDinGVCF() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFWithIBDTest
testMafftfromJava() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
testObjectAssignment() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
TestPHGStuff - Class in net.maizegenetics.pangenome.db_loading
TestPHGStuff() - Constructor for class net.maizegenetics.pangenome.db_loading.TestPHGStuff
testPHGvsKnownSNPs() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
testPHGvsKnownSNPs() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
testPythonLD(String, String, String, String) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
testReadsPerRange() - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
testSimpleGVCFReader() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest: Test of writeToHapmap method, of class ExportUtils.
testSimpleGVCFReader() - Method in class net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2: Test of writeToHapmap method, of class ExportUtils.
testSortedRange() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge
toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
toString() - Method in class net.maizegenetics.pangenome.api.HaplotypePath
toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
toString() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
toString() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
toString() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
totalNumberTaxa() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Returns total number of taxa represented by this graph
transitionProbabilitySameTaxon(double) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
tree(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
tree(Chromosome) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph: Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
TrimGenotypeTableAnchors - Class in net.maizegenetics.pangenome.trimAnchors: Simple class holding utilities to trim a genotype table by identity and coverage thresholds TODO needs to be refractored and have a standardized api Created by zrm22 on 7/6/17.
twoLineNodeCounts(String, String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
twoLineTest(String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils

U

upperPoissonBound() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Upper Poisson Bound used for filtering.
upperPoissonBound(Double) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Upper Poisson Bound.
useBackwardForward() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
useBackwardForward(Boolean) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Set Usebf.
useDepthForCalls() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Boolean flag to have the clustering algorithm use depth information instead of allele counts
useDepthForCalls(Boolean) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Use Depth For Calls.
userid() - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Userid for database
userid(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange: Set Userid.
userid() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Userid for database
userid(String) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin: Set Userid.
userid() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Userid for database
userid(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Set Userid.

V

valueOf(String) - Static method in enum net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE: Returns the enum constant of this type with the specified name.
values() - Static method in enum net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE: Returns an array containing the constants of this enum type, in the order they are declared.
variantContexts() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode: Returns variant contexts for this node.
VariantInfo(HaplotypeNode.VariantInfos, int) - Constructor for class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
variantInfos() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode: These correspond to the VariantContext but holds less information for memory efficiency.
variants() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
vcfDir() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Directory containing vcf files for consensus sequences.
vcfDir(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Set VCF Directory.
vcfDir() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Input genotypes to generate haplotypes from.
vcfDir(String) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Target directory.
vCFFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Normalized VCF file which needs to be corrected
vCFFile(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Set Normalized VCF File.
vCFFileCorrected() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Corrected RefBlock VCF file
vCFFileCorrected(String) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin: Set Output VCF File.
verifyIntervalRanges(String) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
verifySNPEntries(List<String>, String, String) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: This method takes a list of Mummer SNP file entries and verifies the SNP positions are represented in the filtered/overlap-merged coords file.
version() - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Version name for this set of anchors as stored in anchor_versions table in db
version(String) - Method in class net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin: Set Anchor Version.
view(HaplotypeGraph) - Static method in class net.maizegenetics.pangenome.gui.CreateStreamGraph
view(HaplotypeGraph, Multimap<String, HaplotypeNode>) - Static method in class net.maizegenetics.pangenome.gui.CreateStreamGraph
ViewGraphPlugin - Class in net.maizegenetics.pangenome.gui
ViewGraphPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.gui.ViewGraphPlugin

W

weightedMax(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
weightedSum(int, int) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
windowSize() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Window size to add to the extendedBedFile
windowSize(Integer) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin: Set Window Size.
workdir - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
workdir - Static variable in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
workdir - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
writeAnchorsFasta(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphIO: Writes only anchor sequences from HaplotypeNodes in given graph to fasta format.
writeDataToFile(List<Tuple<String, String>>, String, int, BufferedWriter) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
writeFasta(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphIO: Writes all sequences from HaplotypeNodes in given graph to fasta format.
writeFasta(HaplotypeGraph, String, boolean, boolean) - Static method in class net.maizegenetics.pangenome.api.GraphIO
WriteFastaFromGraphPlugin - Class in net.maizegenetics.pangenome.api
WriteFastaFromGraphPlugin(Frame, boolean) - Constructor for class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
writeGraphInfoAllChr(String, int[], HaplotypeGraph, int[][], String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
writeGraphInfoFilesForChr(String, List<HaplotypeNode>, HaplotypeGraph, Map<Integer, Integer>, Map<Integer, Integer>, Chromosome, String) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
writeGraphInfoFilesForChr(String, int[], HaplotypeGraph, Map<Integer, Integer>, Map<Integer, Integer>, Chromosome, String) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
writeInnerAnchorsFasta(HaplotypeGraph, String) - Static method in class net.maizegenetics.pangenome.api.GraphIO: Writes only inner-anchor sequences from HaplotypeNodes in given graph to fasta format.
writeNodeStatistics(HaplotypeGraph, List<HaplotypeNode>, Map<Integer, Integer>, Map<Integer, Integer>, String) - Static method in class net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
writePathInformation(String, List<HaplotypeNode>, HaplotypeGraph, Map<Integer, Integer>, Map<Integer, Integer>) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin: Method is used to write diagnostic information about a path to a file.
writeVariantContextsToVCF(List<VariantContext>, String, String, List<String>) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
writeVariantContextsToVCF(List<VariantContext>, String, String, String) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils: Method to write the list of VariantContexts out to a vcf file.

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