All Classes
AnchorDataPHG
AnchorInfo
AssemblyHaplotypesPlugin
AssemblyProcessingUtils
CloseDBConnectionPlugin
CompareAssembliesToReference
CompareFastaToReference
CompareHaplotypesToAssembly
CompareToKnownSNPPlugin
ComputeMedianAnnotation
ComputeMedianGVCFAndFilter
ComputeNDistribution
ContrastHaplotypeAndAssemblySequence
ConvertGBSToSNPs
ConvertGBSUtils
ConvertRampSeqTagsToMapPlugin
ConvertToHaplotypeCallerInput
CountConsensusTaxaAtRefRange
CountNsInRawHapSequencesPlugin
CreateAnchorFilesFromGeneGFF
CreateBiggerIntervals
CreateContigFastaFromAssemblyGenomePlugin
CreateCSV_TrimmedAnchorLoading
CreateDBLoadScripts
CreateFastaDBFiles
CreateGraphUtils
CreateHaplotypeNodeListFromFasta
CreateHaplotypesFromFasta
CreateHashForFiles
CreateIntervalBedFilesPlugin
CreateIntervalsFile
CreateIntervalsFileFromGffPlugin
CreatePHGPostgresDockerPlugin
CreateStreamGraph
DBLoadingUtils
DBLoadingUtils.AnchorType
DBLoadingUtils.MethodType
EvaluateGVCFbyKnownSNPTest
EvaluateGVCFbyKnownSNPTest2
EvaluateGVCFWithIBDTest
EvaluateHaplotypeFastaInKnownIBDRegions
ExportHaplotypePathToFilePlugin
ExportVCForTaxonMethodPlugin
ExtractFastaFromGVCFCBSU
ExtractFastaUtils
FastqToHapCountPlugin
FastqToKmerCountPlugin
FillIndelsIntoConsensus
FillIndelsIntoConsensus.INDEL_MERGE_RULE
FilterFastqUsingBAMPlugin
FilterGraphPlugin
FilterGVCFPlugin
FilterGVCFSingleFilePlugin
FindHaplotypeClustersPlugin
FindHaplotypeClustersPlugin.CLUSTER_METHOD
FindProteomeGenesInAssembly
FindRampSeqContigsInAssemblies
FindTrimmedAnchorCoordinates
FindTrimmedAssemblyCoordinates
GeneGFFData
GenerateHaplotypeCallerScripts
GenoHaploData
GetDBConnectionPlugin
GetFastaSequenceLengths
GraphIO
GraphUtils
GVCFGenotypeSequence
GVCFSequence
GVCFStats
GVCFTyperPlugin
GVCFTyperPlugin.EMIT_MODE
GVCFUtils
HapCallingUtils
HapCountBestPathPlugin
HapCountBestPathToTextPlugin
HaplotypeEdge
HaplotypeGraph
HaplotypeGraphBuilderPlugin
HaplotypeNode
HaplotypePath
HaplotypeSequence
ImportHaplotypePathFilePlugin
IndexHaplotypeKmersPlugin
LoadConsensusAnchorSequencesPlugin
LoadGenomeIntervalsToPHGdbPlugin
LoadHaplotypeCountsTablePlugin
LoadHapSequencesFromGVCFPlugin
LoadHapSequencesToDBPlugin
MergeGVCFPlugin
MergeGVCFUtils
Mummer4DoonerBZStats
MummerAnalysisMetricsPlugin
MummerScriptProcessing
PathsToVCFPlugin
PathToIgraphPlugin
PHGData
PHGDataWriter
PHGdbAccess
PurgeSequencesFromAlignments
QualityReportAnchorsToHaplotypes
RampSeqContigToGenomeIntervalPlugin
RedirectStreams
ReferenceRange
ReferenceRangeEmissionProbability
ReferenceRangeEmissionProbability.Builder
ReferenceRangeEmissionProbability.METHOD
ReferenceRangeTransitionProbability
RemoveLongRunNs
ResizeRefBlockPlugin
RunGVCFTyper
RunHapCollapsePipelinePlugin
ScoreRangesByInclusionCountsPlugin
ShellScript_createLoadHaplotypes
SimpleGVCFReader
SplitFastaByChromPlugin
SplitMafftRun
SplitVCFIntoIntervalsPlugin
TestPHGStuff
TrimGenotypeTableAnchors
ViewGraphPlugin
WriteFastaFromGraphPlugin