C-index

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

C

calcLevenshtein(String,String,int) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
calculateCoordDistance(Tuple,Tuple) - function in 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.
calculateDistanceMatrix(Map) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
calculateRegionCovered(RangeMap,Range) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Given a map of ranges and a range, calculate the number of positions within the given range that are represented in the RangeMap.
call() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
callSNPsFromHaplotypeNodes(List,HashMap,String,String,String,String) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
callSNPsFromHaplotypePath(HaplotypeGraph,HaplotypePath,String,String,String,String) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
callSNPsFromSomeVCFs(String,String,String,String) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
cancel() - function in net.maizegenetics.plugindef.AbstractPlugin
checkChrom2DupAnchor(String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
checkForEmbedded(List,boolean) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Check entries in a list of mummer4 coords file entries and removed those that are embedded
checkForOverlap(Tuple,Tuple) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Returns a Tuple indicating There will be inversions, so no guarantee prevStartEnd.x is <= curStartEnd.
checkForSeqMatch(String,String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
checkNoListEntriesInRange(HashSet,List) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing: Method takes a RangeSet of Integers and a list of integers.
checkSnpEntryInRange(String,RangeMap,String) - function in 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.
chooseVarIdForSNPPositionFromGenotypeTable(GenotypeTable,Map) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
chrom() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: If a chrom is specified, pull only data for that chromosome.
chrom(String) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Chrom.
chrom() - function in 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) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Chromosome Name.
chrom() - function in net.maizegenetics.pangenome.trimAnchors.AnchorInfo
chromosome() - function in net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
chromosome() - function in net.maizegenetics.pangenome.api.ReferenceRange: Chromosome in the reference genome from which this ReferenceRange originates
chromosome() - function in net.maizegenetics.pangenome.api.Variant
chromosomes() - function in net.maizegenetics.dna.map.GenomeSequence
chromosomes() - function in net.maizegenetics.pangenome.api.HaplotypeGraph
chromosomes() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Chromosomes
chromosomes(List) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Chromosomes.
chromosomes() - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomes() - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSequence(Chromosome) - function in net.maizegenetics.dna.map.GenomeSequence
chromosomeSequence(Chromosome) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence: Unsupported method to get the sequence for the whole chromosome
chromosomeSequence(Chromosome,int,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
chromosomeSequence(Chromosome) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSequence(Chromosome,int,int) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSize(Chromosome) - function in net.maizegenetics.dna.map.GenomeSequence
chromosomeSize(Chromosome) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
chromosomeSize(Chromosome) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
clear() - function in com.google.protobuf.AbstractMessage.Builder
clear() - function in com.google.protobuf.Message.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder
clear() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder
clearAsmContig() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmContig = 6;
clearAsmEndCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 asmEndCoordinate = 8;
clearAsmStartCoordinate() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 asmStartCoordinate = 7;
clearAsmStrand() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: string asmStrand = 9;
clearChromosome() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string chromosome = 3;
clearEdgeProbability() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: double edgeProbability = 3;
clearEnd() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 end = 5;
clearField(Descriptors.FieldDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
clearField(Descriptors.FieldDescriptor) - function in com.google.protobuf.Message.Builder
clearGenomeFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 genomeFileId = 4;
clearGvcfFile() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder: string gvcfFile = 2;
clearGvcfFileId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 gvcfFileId = 5;
clearGvcfIdToFile() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.GVCFIDToFileProto gvcfIdToFile = 4;
clearHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: int32 hapId = 1;
clearHaplotypeEdges() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeEdgeProto haplotypeEdges = 3;
clearHaplotypeNodes() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.HaplotypeNodeProto haplotypeNodes = 2;
clearHaplotypeSequence() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: .net.maizegenetics.pangenome.io.HaplotypeSequenceProto haplotypeSequence = 2;
clearId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.GVCFIDToFileProto.Builder: int32 id = 1;
clearId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 id = 1;
clearLeftHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: int32 leftHapId = 1;
clearLength() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: int32 length = 1;
clearMethods() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: repeated string methods = 6;
clearOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.AbstractMessage.Builder
clearOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.GeneratedMessageV3.Builder
clearOneof(Descriptors.OneofDescriptor) - function in com.google.protobuf.Message.Builder
clearQualityScore() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: double qualityScore = 3;
clearReferenceName() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: string referenceName = 2;
clearReferenceRangeID() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: int32 referenceRangeID = 2;
clearReferenceRanges() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeGraphProto.Builder: repeated .net.maizegenetics.pangenome.io.ReferenceRangeProto referenceRanges = 1;
clearRightHapId() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeEdgeProto.Builder: int32 rightHapId = 2;
clearSeqHash() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeSequenceProto.Builder: string seqHash = 4;
clearStart() - function in net.maizegenetics.pangenome.io.Haplotypegraph.ReferenceRangeProto.Builder: int32 start = 4;
clearTaxa() - function in net.maizegenetics.pangenome.io.Haplotypegraph.HaplotypeNodeProto.Builder: repeated string taxa = 3;
clone() - function in com.google.protobuf.AbstractMessage.Builder
clone() - function in com.google.protobuf.GeneratedMessageV3.Builder
clone() - function in com.google.protobuf.Message.Builder
close() - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
CloseDBConnectionPlugin - class in net.maizegenetics.pangenome.db_loading: This method closes a DB connection.
clusterAssemblies() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster: Method to cluster Assemblies Steps Taken Here: For the current Reference Range, extract out all haplotypes in the graph Compute a distance matrix using #SNPS/(#SNPs+#Ref) as the distance.
clusteringMode() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Clustering mode
clusteringMode(RunHapConsensusPipelinePlugin.CLUSTERING_MODE) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Set Clustering Mode.
clusterMethod() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: The method used to cluster taxa.
clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin: Set Cluster Method.
clusterMethod() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: The method used to cluster taxa.
clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Cluster Method.
clusterSize() - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Cluster size to use with mummer4 nucmer script.
clusterSize(Integer) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Set Mummer4 Nucmer Cluster Size .
clusterThenMerge() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
collapseMethod() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Name of the collapse method to be stored in the database
collapseMethod(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Collapse Method.
collapseMethod() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Name of the collapse method to be stored in the database
collapseMethod(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Set Collapse Method.
collapseMethodDetails() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Details for the collapse method to be stored in the database
collapseMethodDetails(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Collapse Method Details.
collapseMethodDetails() - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Details for the collapse method to be stored in the database
collapseMethodDetails(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin: Set Collapse Method Details.
comparaRawFilteredAlignment(String,String) - function in net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
CompareAssembliesToReference - class in net.maizegenetics.pangenome.hapcollapse: Simple little utility to compare assembly alignments to the reference genome
compareEdges(List,List) - function in net.maizegenetics.pangenome.api.CreateGraphUtils
CompareFastaToReference - class in net.maizegenetics.pangenome: Created by terry on 3/21/17.
CompareHaplotypesToAssembly - class in net.maizegenetics.pangenome: Created by terry on 3/21/17.
compareRefToReAssembledChrom(String,String,String,String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
compareTo(HaplotypeNode) - function in net.maizegenetics.pangenome.api.HaplotypeNode
compareTo(ReferenceRange) - function in net.maizegenetics.pangenome.api.ReferenceRange
compareTo(AnchorDataPHG) - function in net.maizegenetics.pangenome.db_loading.AnchorDataPHG
compareTo(GeneGFFData) - function in net.maizegenetics.pangenome.db_loading.GeneGFFData
compareTo(VariantMappingData) - function in net.maizegenetics.pangenome.db_loading.VariantMappingData
compareTo(RunHapConsensusPipelinePlugin.VariantInfoConsensus) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.VariantInfoConsensus
compareTo(PairedSimilarFragment) - function in net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
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.
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.
ComputeMedianGVCFAndFilter - class in net.maizegenetics.pangenome.gvcfFiltering: TODO Separate Filter from FastaExtraction Created by zrm22 on 7/18/17.
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.
confident - enum entry in net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE
configFile() - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Database configuration file
configFile(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: Set Database Config File.
configFile() - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin
configFile(String) - function in net.maizegenetics.pangenome.api.MethodTableReportPlugin
configFile() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin: Path to config file for db loading
configFile(String) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin: Set config file for db access
configFile() - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin: Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
configFile(String) - function in net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin: Set DataBase Configuration File.
configFile() - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin: Configuration file
configFile(String) - function in net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin: Set Config File.
configFile() - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: Set DB Config Files.
configFile() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Config folder containing the filtering parameters.
configFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin: Set Config File.
configFile() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Config folder containing the filtering parameters.
configFile(String) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin: Set Config File.
configFile() - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Config file that specifies database connection parameters
configFile(String) - function in net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin: Set Config File.
configFile() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Database configuration file
configFile(String) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin: Set Database Config File.
configFile() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Database configuration file
configFile(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Database Config File.
configFile() - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin: Config file that specifies database connection parameters
configFile(String) - function in net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin: Set Config File.
configFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set DB Config File.
configFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
configFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set DB Config File.
connection(String) - function in net.maizegenetics.pangenome.api.CreateGraphUtils: Creates a database connection given a properties file
connection(String,String,String,String) - function in net.maizegenetics.pangenome.api.CreateGraphUtils: Creates a sqlite database connection.
connection(boolean) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils: Creates a database connection from the TASSEL ParameterCache It is expected that only initial db loading methods will call this with "createNew" = true.
connection(String,boolean) - function in 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) - function in 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.
CONSENSUS_ANCHOR_SEQUENCE - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType
consensusFastaOutputDir() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Directory where you want to store the output fastas from the consensus process
consensusFastaOutputDir(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Consensus Fasta Output Dir.
ConsensusProcessingUtils - class in net.maizegenetics.pangenome.hapcollapse: This class holds methods for processing consensus using the variants and alleles tables or data derived from them.
consensusVariants(Map,List,ReferenceRange) - function in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
consensusVCFOutputDir() - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Directory where you want to store the output VCFs from the consensus process
consensusVCFOutputDir(String) - function in net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin: Set Consensus VCF Output Dir.
conservedGeneFile() - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin: File containing list of conserved genes to include as anchor regions
conservedGeneFile(String) - function in net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin: Set Conserved Gene File.
contigBAM() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin: Name of contig BAM file to process
contigBAM(String) - function in 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).
convert(String,Class) - function in net.maizegenetics.plugindef.AbstractPlugin
convertCSVToBed(Array) - function in net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
convertCSVToIntervals(Array) - function in net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
convertMethods(String) - function in net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
ConvertRampSeqTagsToMapPlugin - class in net.maizegenetics.pangenome.hapCalling: Created by zrm22 on 10/4/17.
ConvertReadsToPathUsingHMM - class in net.maizegenetics.pangenome.hapCalling
ConvertToHaplotypeCallerInput - class in net.maizegenetics.pangenome
convertVariantsToSequence(List,ReferenceRange,GenomeSequence) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
convertVCFToGVCF(List) - function in net.maizegenetics.pangenome.hapcollapse.GVCFUtils
coordsFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Output of Mummer coords file
coordsFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats: Set Mummer Coords File.
coordsFile() - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Output of Mummer coords file
coordsFile(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin: Set Mummer Coords File.
countMethod() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: The haplotype count method name assigned when the counts were created and stored in the DB.
countMethod(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin: Set Haplotype count method name.
countNsInFasta() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
CountNsInRawHapSequencesPlugin - class in net.maizegenetics.pangenome.pipelineTests: NOTE: THis test is obsolete - uses old schema and old connection method.
coverage - enum entry in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD
create(int,int,double,double,int,int,int,int,double,double,double) - function in net.maizegenetics.pangenome.smallseq.CreateTestGenomes
createAlleleList(VariantContext) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: createALleleList returns an array list containing just the ref allele string, if the VariantContext record is a ref record.
createAlleleList(HaplotypeNode.VariantInfo) - function in net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils: Method to create a list of alleles based on if the variant info is a ref or variant.
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.
createAndLoadAssemblyData(Map,List,GenomeSequence,Connection,String,String,int,String,Map) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin: Create the assembly genotype/haplotype data and load to the PHG database
createAsmCoordinatesRangeMap(Map) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Creates a RangeMap of asm positions from the given reference range map, using lower reference position as the value.
CreateBiggerIntervals - class in net.maizegenetics.pangenome.db_loading
CreateContigFastaFromAssemblyGenomePlugin - class in net.maizegenetics.pangenome.processAssemblyGenomes: The sequence for each chromosome in the genome fasta file will be split based on N's.
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.
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.
createDistanceMatrix(int,Chromosome,ReferenceRange,TaxaList,Map) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils: Function to create a disntance matrix given a set of variants for a single reference range.
createEdges(Collection) - function in net.maizegenetics.pangenome.api.CreateGraphUtils: Generates Edges based on HaplotypeNodes.
createEdges(List,List) - function in net.maizegenetics.pangenome.api.CreateGraphUtils
createEdges(NavigableMap) - function in net.maizegenetics.pangenome.api.CreateGraphUtils
CreateFastaDBFiles - class in net.maizegenetics.pangenome.fastaExtraction: Simple one off command line tool to create the necessary files to upload fastas to the db.
createFiles(String,String) - function in net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
createFindProteomeFile() - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff
createGATKGVCFHeader(List) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
CreateGeneIntervalsFromConservedGFFPlugin - class in net.maizegenetics.pangenome.db_loading: Creates bed file with chromosome and coordinates to be used to create PHG reference ranges.
createGenericHeader(List) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
createGenericHeaderLineSet() - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
createGenotypeTableFromGVCFs(ReferenceRange,Multimap,GenomeSequence) - function in 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,GenomeSequence) - function in net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils: Method to make a genotypeTable from a list of Haplotype Nodes.
CreateGraphUtils - class in net.maizegenetics.pangenome.api
createGtvalueMap() - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
createGVCFBlockHeaderLine(int,int) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
createHapIdToFileNameMapping(HaplotypeGraph,String) - function in net.maizegenetics.pangenome.hapCalling.HapCallingUtils
createHaplotypeNodeList(String,String) - function in net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
createHaplotypeNodeListFromDirectory(String,String) - function in 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.
createHaplotypeNodes(Connection,List,boolean,boolean,SortedSet,List,TaxaList) - function in net.maizegenetics.pangenome.api.CreateGraphUtils
createHaplotypeNodes(Connection,Map,Map,List,boolean,boolean,SortedSet,List,TaxaList) - function in net.maizegenetics.pangenome.api.CreateGraphUtils
createHaplotypeNodesWithVariants(Connection,Set) - function in net.maizegenetics.pangenome.api.CreateGraphUtils: Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.
createHaplotypeNodesWithVariants(Connection,HaplotypeGraph) - function in 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.
CreateHashForFiles - class in net.maizegenetics.pangenome.Utils: This class creates the MD4 or SHA-1 hash for a specified file.
createInbredFiles(String,String) - function in net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
createInitialAlleles(int) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils: This method creates a list of allele strings based on the allele set of A,C,G,T,N The size of the set will be 5 + 5^2 + 5^3 + ...
CreateIntervalBedFilesPlugin - class in net.maizegenetics.pangenome.db_loading: Created by zrm22 on 1/16/18.
CreateIntervalsFile - class in net.maizegenetics.pangenome.db_loading: This method must be re-worked - getHaplotypeAnchorCoordinates no longer accesses the correct tables.
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.
createLoadScript(String,String,String,String,String,String) - function in net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts: Method which will create the loading script based on the input files.
createNew() - function in 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) - function in net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin: Set Create New DB.
createPathNodesForGameteGrp(String,Connection,int) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils: This method connects to a database, finds the haplotypes for a specific gamete group, and creates an ordered-by-ref-range list of haplotype ids.
CreatePHGPostgresDockerPlugin - class in net.maizegenetics.pangenome.db_loading: This plugin will create the phg_postgres docker if it doesn't exist.
createRefRangeVC(GenomeSequence,String,Position,Position,Position,Position) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Helper method to create a Reference Range VariantContext for assemblies.
CreateSmallGenomesPlugin - class in net.maizegenetics.pangenome.smallseq: This class provides a standalone plugin to create the small sequence test genome files.
createSNPVC(String,Position,Position,Tuple,Position,Position) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Helper method to create a SNP Variant context for assemblies.
CreateStreamGraph - class in net.maizegenetics.pangenome.gui
CreateTestGenomes - class in net.maizegenetics.pangenome.smallseq
createTrimmedFastaGenotypeTable(String,String,double,double,int,int,int,int) - function in 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) - function in net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors: Method which will create a trimmed GenotypeTable based on the gene start and end positions
createVarIDtoRefAltData(Map) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils: Returns a map of variantID to RefAltData for each variantId/data lookup.
createVCasRefBlock(GenomeSequence,String,RangeSet,Map) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils: Method to build list of VariantContexts as RefRangeVCs - used when the reference and assembly have identical chromosome data
createVinfoObject(HaplotypeNode.VariantInfo) - function in net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG

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