- GenerateHaplotypeCallerScripts
- GetFastaSequenceLengths
- GVCFStats
- CompareFastaToReference
- CompareHaplotypesToAssembly
- ConvertToHaplotypeCallerInput
- ComputeNDistribution
- SplitMafftRun
- RemoveLongRunNs
- DBLoadingUtils
- CreatePHGPostgresDockerPlugin
- GenoHaploData
- VariantMappingData
- GetDBConnectionPlugin
- GeneGFFData
- CreateIntervalBedFilesPlugin
- CreateBiggerIntervals
- VariantsProcessingUtils
- FindTrimmedAssemblyCoordinates
- CreateIntervalsFileFromGffPlugin
- AddRefRangeAsAssemblyPlugin
- CreateGeneIntervalsFromConservedGFFPlugin
- DatabaseSummaryPlugin
- AddRefRangeGroupPlugin
- CloseDBConnectionPlugin
- SplitFastaByChromPlugin
- PHGDataWriter
- PHGdbAccess
- FindTrimmedAnchorCoordinates
- CreateAnchorFilesFromGeneGFF
- CreateIntervalsFile
- CreateCSV_TrimmedAnchorLoading
- TestPHGStuff
- PHGData
- ShellScript_createLoadHaplotypes
- AnchorDataPHG
- AssemblyProcessingUtils
- MummerScriptProcessing
- ResizeRefBlockPlugin
- PairedSimilarFragment
- AssemblyHaplotypesPlugin
- FindRampSeqContigsInAssemblies
- RampSeqContigToGenomeIntervalPlugin
- MummerAnalysisMetricsPlugin
- SyntenicAnchors
- CreateContigFastaFromAssemblyGenomePlugin
- RedirectStreams
- Mummer4DoonerBZStats
- ComputeMedianAnnotation
- ComputeMedianGVCFAndFilter
- FilterGVCFSingleFilePlugin
- SplitVCFIntoIntervalsPlugin
- FilterGVCFPlugin
- CompareToKnownSNPPlugin
- GenerateRForPHG
- HaplotypesDataVectors
- HaplotypesDataMetricsPlugin
- ContrastHaplotypeAndAssemblySequence
- EvaluateHaplotypeFastaInKnownIBDRegions
- CountNsInRawHapSequencesPlugin
- FindProteomeGenesInAssembly
- RefRangeVectors
- Haplotypegraph
- CreateHashForFiles
- CreateSmallGenomesPlugin
- SmallSeqPaths
- CreateTestGenomes
- MergeGVCFUtils
- FillIndelsIntoConsensus
- PurgeSequencesFromAlignments
- RunGVCFTyper
- RunHapConsensusPipelinePlugin
- CreateHaplotypesFromFasta
- QualityReportAnchorsToHaplotypes
- CompareAssembliesToReference
- RefAltData
- MergeGVCFPlugin
- ConsensusProcessingUtils
- GVCFUtils
- FindHaplotypeClustersPlugin
- RunHapCollapsePipelinePlugin
- GVCFTyperPlugin
- CreateStreamGraph
- ViewGraphPlugin
- ReferenceRangeTransitionProbability
- RMethods
- DBVariant
- FilterGraphPlugin
- Variant
- WriteFastaFromGraphPlugin
- AlleleInfo
- HaplotypeGraph
- CreateGraphUtils
- HaplotypeNode
- CreateHaplotypeNodeListFromFasta
- HaplotypeSequence
- GraphUtils
- HaplotypeGraphBuilderPlugin
- VariantUtils
- GraphIO
- HaplotypeEdge
- HaplotypePath
- ReferenceRange
- MethodTableReportPlugin
- ReferenceRangeEmissionProbability
- CreateDBLoadScripts
- ExtractFastaFromGVCFCBSU
- GVCFGenotypeSequence
- ExtractFastaUtils
- GVCFSequence
- CreateFastaDBFiles
- AnchorInfo
- TrimGenotypeTableAnchors
- ExportHaplotypePathToFilePlugin
- HapCountBestPathToTextPlugin
- ScoreRangesByInclusionCountsPlugin
- ImportHaplotypePathFilePlugin
- HapCountBestPathPlugin
- FastqToKmerCountPlugin
- PathToIgraphPlugin
- IndexHaplotypeKmersPlugin
- HapCallingUtils
- ExportVCForTaxonMethodPlugin
- FilterFastqUsingBAMPlugin
- ConvertReadsToPathUsingHMM
- ConvertRampSeqTagsToMapPlugin