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Package Hierarchies:
net.maizegenetics.pangenome
,
net.maizegenetics.pangenome.Utils
,
net.maizegenetics.pangenome.annotations
,
net.maizegenetics.pangenome.api
,
net.maizegenetics.pangenome.db_loading
,
net.maizegenetics.pangenome.db_updateDelete
,
net.maizegenetics.pangenome.fastaExtraction
,
net.maizegenetics.pangenome.gui
,
net.maizegenetics.pangenome.gvcfFiltering
,
net.maizegenetics.pangenome.hapCalling
,
net.maizegenetics.pangenome.hapcollapse
,
net.maizegenetics.pangenome.io
,
net.maizegenetics.pangenome.liquibase
,
net.maizegenetics.pangenome.multiSequenceAlignment
,
net.maizegenetics.pangenome.pipeline
,
net.maizegenetics.pangenome.pipelineTests
,
net.maizegenetics.pangenome.processAssemblyGenomes
,
net.maizegenetics.pangenome.smallseq
,
net.maizegenetics.pangenome.trimAnchors
Class Hierarchy
net.maizegenetics.pangenome.hapCalling.
ImportDiploidPathPlugin
net.maizegenetics.pangenome.api.
HaplotypeNode.VariantInfo
net.maizegenetics.pangenome.hapcollapse.
MergeGVCFUtils
net.maizegenetics.pangenome.api.
MethodTableReportPlugin
net.maizegenetics.pangenome.api.
HaplotypeEmissionProbabilityKt
net.maizegenetics.pangenome.pipelineTests.
GenerateRForPHG
net.maizegenetics.pangenome.api.
AddPathsToGraphPluginKt
net.maizegenetics.pangenome.api.
HaplotypeEmissionProbability
net.maizegenetics.pangenome.db_loading.
AnchorDataPHG
net.maizegenetics.pangenome.hapCalling.
DiploidTransitionProbabilityWithInbreeding
net.maizegenetics.pangenome.db_loading.
CreateCSV_TrimmedAnchorLoading
net.maizegenetics.pangenome.hapCalling.
MostLikelyParents
net.maizegenetics.pangenome.processAssemblyGenomes.
SplitASMContigsByLengthPluginKt
net.maizegenetics.pangenome.pipelineTests.
EvaluateHaplotypeFastaInKnownIBDRegions
net.maizegenetics.pangenome.db_loading.
ChangeDBMethodTypePlugin
net.maizegenetics.pangenome.api.
GraphSpliterator
net.maizegenetics.pangenome.pipelineTests.
CompareToKnownSNPPlugin
net.maizegenetics.pangenome.hapcollapse.
QualityReportAnchorsToHaplotypes
net.maizegenetics.pangenome.db_loading.
VariantLoadingUtilsKt
net.maizegenetics.pangenome.hapCalling.
PathsToVCFPlugin
net.maizegenetics.pangenome.api.
DBVariant
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
AlterNucmerFirstLinePlugin
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPlugin.RefRangeStats
net.maizegenetics.pangenome.hapcollapse.
CompareAssembliesToReference
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPlugin
net.maizegenetics.pangenome.api.
ReferenceRangeSummaryPlugin
net.maizegenetics.pangenome.hapCalling.
KmerMap
net.maizegenetics.pangenome.hapCalling.
MutableKmerCounter
net.maizegenetics.pangenome.hapCalling.
MutableKmerToIdMap
net.maizegenetics.pangenome.
GenerateHaplotypeCallerScripts
net.maizegenetics.pangenome.api.
HaplotypeEdge
net.maizegenetics.pangenome.hapcollapse.
ProfileMxdivPlugin.ProfileInput
net.maizegenetics.pangenome.hapcollapse.
PurgeSequencesFromAlignments
net.maizegenetics.pangenome.api.
CreateTestGraphKt
net.maizegenetics.pangenome.hapCalling.
GraphIdMaps
net.maizegenetics.pangenome.hapcollapse.
RunHapConsensusPipelinePlugin.RunMergeAndCluster
net.maizegenetics.pangenome.processAssemblyGenomes.
CreateContigFastaFromAssemblyGenomePlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
net.maizegenetics.pangenome.processAssemblyGenomes.
ResizeRefBlockPlugin
net.maizegenetics.pangenome.multiSequenceAlignment.
ComputeNDistribution
net.maizegenetics.pangenome.db_loading.
AddTaxaToTaxaGroupPlugin
net.maizegenetics.pangenome.hapcollapse.
RunGVCFTyper
net.maizegenetics.pangenome.gui.
CreateStreamGraph
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin.PathFindingInput
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypeKmersPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
FindRampSeqContigsInAssemblies
net.maizegenetics.pangenome.pipeline.
SAMAlignmentMetricsPlugin.ReadNameData
net.maizegenetics.pangenome.db_loading.
ShellScript_createLoadHaplotypes
net.maizegenetics.pangenome.processAssemblyGenomes.
MummerScriptProcessing
net.maizegenetics.pangenome.hapCalling.
PathToIgraphPlugin
net.maizegenetics.pangenome.hapCalling.
FastqToHapCountMinimapPluginKt
net.maizegenetics.pangenome.api.
ReferenceRange
net.maizegenetics.pangenome.liquibase.
CheckDBVersionPlugin
net.maizegenetics.pangenome.pipeline.
LiquibaseCommandPlugin
net.maizegenetics.pangenome.db_loading.
ReadMappingDBRecord
net.maizegenetics.pangenome.gvcfFiltering.
FilterGVCFPlugin
net.maizegenetics.pangenome.annotations.
PathToGFFPlugin
net.maizegenetics.pangenome.hapCalling.
SingleHapMapping
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPlugin.AssemblyVariantInfo
net.maizegenetics.pangenome.api.
RPHGMethodsKotlin.HaplotypeSequences
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPluginKt
net.maizegenetics.pangenome.hapCalling.
HapCallingUtils
net.maizegenetics.pangenome.hapCalling.
DiploidTransitionProbability
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPlugin.ReadMappingResult
net.maizegenetics.pangenome.hapCalling.
RefRangeWrapper
net.maizegenetics.pangenome.pipeline.
CreateRefRangeUtils.RegionInputData
net.maizegenetics.pangenome.hapCalling.
FastqToHapCountMinimapPlugin
net.maizegenetics.pangenome.api.
WriteFastaFromGraphPlugin
net.maizegenetics.pangenome.db_loading.
TestPHGStuff
net.maizegenetics.pangenome.api.
Method
net.maizegenetics.pangenome.api.
HaplotypeGraphStreamBuilderPlugin.Companion
net.maizegenetics.pangenome.api.
RMethods.DataFrameVectors
net.maizegenetics.pangenome.pipeline.
CreateRefRangeUtils
net.maizegenetics.pangenome.hapcollapse.
CentroidPathFromGraphPlugin
net.maizegenetics.pangenome.pipelineTests.
HaplotypesDataVectors
net.maizegenetics.pangenome.db_loading.
VariantMappingData
net.maizegenetics.pangenome.api.
CreateHaplotypeNodeListFromFasta
net.maizegenetics.pangenome.hapcollapse.
ProfileMxdivPlugin
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin
net.maizegenetics.pangenome.hapCalling.
HapCountBestPathToTextPlugin
net.maizegenetics.pangenome.db_loading.
HaplotypeGeneMetricsPluginKt
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin
net.maizegenetics.pangenome.hapcollapse.
GVCFUtils
net.maizegenetics.pangenome.processAssemblyGenomes.
SplitASMContigsByLengthPlugin
net.maizegenetics.pangenome.pipelineTests.
FindProteomeGenesInAssembly
net.maizegenetics.pangenome.hapCalling.
HapIdSetCount
net.maizegenetics.pangenome.hapCalling.
SAMToMappingPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesPlugin
net.maizegenetics.pangenome.multiSequenceAlignment.
SplitMafftRun
net.maizegenetics.pangenome.hapcollapse.
RunHapConsensusPipelinePlugin
net.maizegenetics.pangenome.hapcollapse.
KmerBasedConsensusUtils
net.maizegenetics.pangenome.liquibase.
LiquibaseUpdatePlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesMultiThreadPluginKt
net.maizegenetics.pangenome.hapCalling.
KmerUtils
net.maizegenetics.pangenome.api.
ExportGFAKt
net.maizegenetics.pangenome.db_loading.
AddRefRangeAsAssemblyPlugin
net.maizegenetics.pangenome.hapCalling.
IndexKmerByHammingPlugin
net.maizegenetics.pangenome.gui.
ViewGraphPlugin
net.maizegenetics.pangenome.hapCalling.
FastqToKmerCountPlugin
net.maizegenetics.pangenome.hapCalling.
FilterFastqUsingBAMPlugin
net.maizegenetics.pangenome.hapCalling.
CreateHapIdMapsPlugin
net.maizegenetics.pangenome.pipeline.
PopulatePHGDBPipelinePluginKt
net.maizegenetics.pangenome.db_loading.
DBLoadingUtils
net.maizegenetics.pangenome.hapCalling.
SplitKeyFilePlugin
net.maizegenetics.pangenome.hapCalling.
Minimap2Utils
net.maizegenetics.pangenome.hapCalling.
SNPToReadMappingPluginKt
net.maizegenetics.pangenome.db_loading.
DatabaseSummaryPlugin
net.maizegenetics.pangenome.fastaExtraction.
CreateFastaDBFiles
net.maizegenetics.pangenome.api.
ConvertVariantContextToVariantInfo
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPluginKt
net.maizegenetics.pangenome.api.
HaplotypePath
net.maizegenetics.pangenome.db_loading.
LoadHaplotypesFromGVCFPluginKt
net.maizegenetics.pangenome.api.
RMethods
net.maizegenetics.pangenome.gvcfFiltering.
ComputeMedianAnnotation
net.maizegenetics.pangenome.db_updateDelete.
DeletePathsPlugin
net.maizegenetics.pangenome.hapCalling.
FindBestDiploidPathKt
net.maizegenetics.pangenome.api.
RMethods.MatrixWithNames
net.maizegenetics.pangenome.hapCalling.
SecondaryStats
net.maizegenetics.pangenome.io.
SFTPConnection
net.maizegenetics.pangenome.hapCalling.
FastqToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
KeyFileUniqueRecord
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesMultiThreadPlugin
net.maizegenetics.pangenome.db_loading.
CreateIntervalsFileFromGffPlugin
net.maizegenetics.pangenome.api.
VariantUtils
net.maizegenetics.pangenome.hapCalling.
KmerToRefRangeIdToPurgeArray
net.maizegenetics.pangenome.processAssemblyGenomes.
RetrieveGenomeFileDataPluginKt
net.maizegenetics.pangenome.db_loading.
HaplotypeGeneMetricsPlugin
net.maizegenetics.pangenome.hapCalling.
ImportReadMappingToDBPluginKt
net.maizegenetics.pangenome.api.
HaplotypeNode
net.maizegenetics.pangenome.hapCalling.
ReadMappingUtils
net.maizegenetics.pangenome.hapcollapse.
FillIndelsIntoConsensus
net.maizegenetics.pangenome.db_loading.
AddRefRangeGroupPlugin
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPluginKt
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.PathFindingResult
net.maizegenetics.pangenome.processAssemblyGenomes.
GVCFBedfileMetricPluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
MafUtils
net.maizegenetics.pangenome.fastaExtraction.
GVCFSequence
net.maizegenetics.pangenome.fastaExtraction.
GVCFGenotypeSequence
net.maizegenetics.pangenome.processAssemblyGenomes.
RedirectStreams
net.maizegenetics.pangenome.db_loading.
CreateIntervalsFile
net.maizegenetics.pangenome.pipeline.
ComparatorTriple
net.maizegenetics.pangenome.pipeline.
ImputePipelinePlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyConsensusMetricPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
Mummer4DoonerBZStats
net.maizegenetics.pangenome.db_loading.
CreateGeneIntervalsFromConservedGFFPlugin
net.maizegenetics.pangenome.hapCalling.
PathFinderForSingleTaxonNodesFactory
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
SyntenicAnchors
net.maizegenetics.pangenome.pipeline.
BuildSLURMBatchScriptPlugin
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPluginKt
net.maizegenetics.pangenome.hapcollapse.
RankingFilePluginKt
net.maizegenetics.pangenome.api.
ASMVariantInfo
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyProcessingUtils
net.maizegenetics.pangenome.pipeline.
MakeDefaultDirectoryPluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyConsensusMetricPluginKt
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin.PathFindingResult
net.maizegenetics.pangenome.hapCalling.
HapCountBestPathPlugin
net.maizegenetics.pangenome.hapCalling.
CreateHapIdMapsPluginKt
net.maizegenetics.pangenome.smallseq.
CreateTestGenomes
net.maizegenetics.pangenome.api.
GraphIO
net.maizegenetics.pangenome.hapCalling.
VerifyPathsPlugin
net.maizegenetics.pangenome.io.
PHGtoGFAv1Plugin
net.maizegenetics.pangenome.gvcfFiltering.
FilterGVCFSingleFilePlugin
net.maizegenetics.pangenome.db_loading.
CreatePHGPostgresDockerPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
RampSeqContigToGenomeIntervalPlugin
net.maizegenetics.pangenome.
CompareHaplotypesToAssembly
net.maizegenetics.pangenome.processAssemblyGenomes.
MafUtilsKt
net.maizegenetics.pangenome.hapcollapse.
CreateHaplotypesFromFasta
net.maizegenetics.pangenome.processAssemblyGenomes.
AlterNucmerFirstLinePluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
PairedSimilarFragment
net.maizegenetics.pangenome.hapcollapse.
ConsensusProcessingUtils
net.maizegenetics.pangenome.db_updateDelete.
DeleteReadMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
MergeFastqPlugin
net.maizegenetics.pangenome.db_loading.
LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
net.maizegenetics.pangenome.gvcfFiltering.
SplitVCFIntoIntervalsPlugin
net.maizegenetics.pangenome.hapCalling.
PositionToRefAndAltHaplotypes
net.maizegenetics.pangenome.api.
GraphUtils
net.maizegenetics.pangenome.db_updateDelete.
DeletePathsPluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyMAFFromAnchorWavePlugin
net.maizegenetics.pangenome.pipeline.
PipelineUtilsKt
net.maizegenetics.pangenome.pipeline.
CreateRefRangesPluginKt
net.maizegenetics.pangenome.hapCalling.
HapIdStats
net.maizegenetics.pangenome.db_loading.
LoadHaplotypesFromGVCFPlugin
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaPlugin
net.maizegenetics.pangenome.hapcollapse.
RankingFilePlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHapMetricPlugin
net.maizegenetics.pangenome.hapCalling.
SNPToReadMappingPlugin
net.maizegenetics.pangenome.pipeline.
BuildSLURMBatchScriptPluginKt
net.maizegenetics.pangenome.pipeline.
CreateRefRangesPlugin
net.maizegenetics.pangenome.api.
GraphToGenotypeTable
net.maizegenetics.pangenome.pipeline.
CreateRefRangeUtils.RegionHaplotypeCount
net.maizegenetics.pangenome.api.
ReferenceRangeEmissionProbability.Builder
net.maizegenetics.pangenome.api.
WriteGraphAsGFAPlugin
net.maizegenetics.pangenome.hapCalling.
VerifyPathsPluginKt
net.maizegenetics.pangenome.api.
FilterGraphPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPlugin.AlignmentBlock
net.maizegenetics.pangenome.api.
ReadMethodTablePlugin
net.maizegenetics.pangenome.hapcollapse.
RunHapConsensusPipelinePlugin.VariantInfoConsensus
net.maizegenetics.pangenome.io.
FastaIO
net.maizegenetics.pangenome.api.
RPHGMethodsKotlin
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPluginKt
net.maizegenetics.pangenome.hapCalling.
ScoreRangesByInclusionCountsPlugin
net.maizegenetics.pangenome.pipeline.
SAMAlignmentMetricsPluginKt
net.maizegenetics.pangenome.multiSequenceAlignment.
RemoveLongRunNs
net.maizegenetics.pangenome.Utils.
CreateHashForFiles
net.maizegenetics.pangenome.db_loading.
LoadAllIntervalsToPHGdbPlugin
net.maizegenetics.pangenome.api.
ReferenceRangeTransitionProbability
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyMAFFromAnchorWavePlugin.InputChannelData
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypesBySNPPlugin
net.maizegenetics.pangenome.pipeline.
ImputePipelinePluginKt
net.maizegenetics.pangenome.fastaExtraction.
ExtractFastaFromGVCFCBSU
net.maizegenetics.pangenome.pipeline.
MakeInitialPHGDBPipelinePluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPlugin.MAFRecord
net.maizegenetics.pangenome.processAssemblyGenomes.
CreateASMCoordsUpdateFilesPlugin.UpdateData
net.maizegenetics.pangenome.pipeline.
PopulatePHGDBPipelinePlugin
net.maizegenetics.pangenome.pipelineTests.
CountNsInRawHapSequencesPlugin
net.maizegenetics.pangenome.db_loading.
CreateBiggerIntervals
net.maizegenetics.pangenome.api.
HaplotypeGraphStream
net.maizegenetics.pangenome.hapcollapse.
ProfileMxdivPluginKt
net.maizegenetics.pangenome.hapCalling.
SimulatedReadsPlugin
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaConverter
net.maizegenetics.pangenome.processAssemblyGenomes.
CreateASMCoordsUpdateFilesPluginKt
net.maizegenetics.pangenome.api.
AddPathsToGraphPlugin
net.maizegenetics.pangenome.hapCalling.
ExportVCForTaxonMethodPlugin
net.maizegenetics.pangenome.hapCalling.
ConvertRampSeqTagsToMapPlugin
net.maizegenetics.pangenome.hapCalling.
ExportHaplotypePathToFilePlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
GVCFBedfileMetricPlugin
net.maizegenetics.pangenome.trimAnchors.
AnchorInfo
net.maizegenetics.pangenome.db_loading.
FindTrimmedAssemblyCoordinates
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPlugin.AlignmentSummary
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyMAFFromAnchorWavePluginKt
net.maizegenetics.pangenome.hapCalling.
FastqDirToMappingPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHapMetricPluginKt
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypesBySNPPluginKt
net.maizegenetics.pangenome.db_loading.
SplitFastaByChromPlugin
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin.VCFSummary
net.maizegenetics.pangenome.smallseq.
CreateSmallGenomesPlugin
net.maizegenetics.pangenome.db_loading.
CreateIntervalBedFilesPlugin
net.maizegenetics.pangenome.pipelineTests.
RefRangeVectors
net.maizegenetics.pangenome.pipeline.
SAMAlignmentMetricsPlugin
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
ScorePafFileByNMThresholdPluginKt
net.maizegenetics.pangenome.hapCalling.
GraphIdMapsKt
net.maizegenetics.pangenome.processAssemblyGenomes.
CreateASMCoordsUpdateFilesPlugin.RefRangeData
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
net.maizegenetics.pangenome.smallseq.
SmallSeqPaths
net.maizegenetics.pangenome.hapCalling.
FastqDirToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin.IndelDistributions
net.maizegenetics.pangenome.hapCalling.
PathsToVCFHaplotypesPlugin
net.maizegenetics.pangenome.annotations.
GFFUtilsKt
net.maizegenetics.pangenome.api.
Variant
net.maizegenetics.pangenome.hapCalling.
GetHapIdsForTaxonPlugin
net.maizegenetics.pangenome.hapcollapse.
GVCFTyperPlugin
net.maizegenetics.pangenome.pipeline.
LiquibaseCommandPluginKt
net.maizegenetics.pangenome.processAssemblyGenomes.
RetrieveGenomeFileDataPlugin
net.maizegenetics.pangenome.db_loading.
GZipCompression
net.maizegenetics.pangenome.hapCalling.
DiploidEmissionProbability
net.maizegenetics.pangenome.hapcollapse.
MergeGVCFPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesMultiThreadPlugin.InputChannelData
net.maizegenetics.pangenome.pipelineTests.
HaplotypesDataMetricsPlugin
net.maizegenetics.pangenome.api.
AlleleInfo
net.maizegenetics.pangenome.annotations.
PathToGFFPluginKt
net.maizegenetics.pangenome.liquibase.
LiquibaseUpdatePluginKt
net.maizegenetics.pangenome.pipeline.
MakeInitialPHGDBPipelinePlugin
net.maizegenetics.pangenome.db_loading.
PHGdbAccess
(implements net.maizegenetics.pangenome.db_loading.
PHGDataWriter
)
net.maizegenetics.pangenome.api.
HaplotypeSequence
net.maizegenetics.pangenome.trimAnchors.
TrimGenotypeTableAnchors
net.maizegenetics.pangenome.api.
BuildGraphFromPathsPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.
ScorePafFileByNMThresholdPlugin
net.maizegenetics.pangenome.db_loading.
GenoHaploData
net.maizegenetics.pangenome.db_loading.
CreateAnchorFilesFromGeneGFF
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaPluginKt
net.maizegenetics.pangenome.hapCalling.
ReadMappingDecoder
net.maizegenetics.pangenome.db_updateDelete.
DeleteReadMappingPlugin
net.maizegenetics.pangenome.hapCalling.
DiploidCountsToPath
net.maizegenetics.pangenome.api.
CreateGraphUtils
net.maizegenetics.pangenome.hapCalling.
ReadMappingKeyFileParsed
net.maizegenetics.pangenome.db_loading.
FindTrimmedAnchorCoordinates
net.maizegenetics.pangenome.db_loading.
VariantsProcessingUtils
net.maizegenetics.pangenome.processAssemblyGenomes.
MummerAnalysisMetricsPlugin
net.maizegenetics.pangenome.api.
BuildGraphFromPathsPlugin.RefrangeInfo
net.maizegenetics.pangenome.hapCalling.
LikelyParentsPlugin
net.maizegenetics.pangenome.
GetFastaSequenceLengths
net.maizegenetics.pangenome.api.
HaplotypeGraph
net.maizegenetics.pangenome.processAssemblyGenomes.
CreateASMCoordsUpdateFilesPlugin
net.maizegenetics.pangenome.db_loading.
CreateValidIntervalsFilePlugin
net.maizegenetics.pangenome.hapCalling.
SplitKeyFilePluginKt
net.maizegenetics.pangenome.hapcollapse.
RunHapCollapsePipelinePlugin
net.maizegenetics.pangenome.hapCalling.
ImportReadMappingToDBPlugin
net.maizegenetics.pangenome.db_loading.
GetDBConnectionPlugin
net.maizegenetics.pangenome.hapCalling.
MergeFastqPluginKt
net.maizegenetics.pangenome.hapCalling.
BestAlignmentGroup
net.maizegenetics.pangenome.
CompareFastaToReference
net.maizegenetics.pangenome.db_loading.
ChangeDBMethodTypePluginKt
net.maizegenetics.pangenome.hapCalling.
FastqToMappingPlugin
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.PathFindingInput
net.maizegenetics.pangenome.db_loading.
LoadAllIntervalsToPHGdbPluginKt
net.maizegenetics.pangenome.hapCalling.
ViterbiForDiploidPath
net.maizegenetics.pangenome.pipeline.
MakeDefaultDirectoryPlugin
net.maizegenetics.pangenome.hapCalling.
PathFinderForSingleTaxonNodes
net.maizegenetics.pangenome.hapcollapse.
ProfileMxdivPlugin.ProfileResult
net.maizegenetics.pangenome.db_loading.
CreateValidIntervalsFilePluginKt
net.maizegenetics.pangenome.pipelineTests.
ContrastHaplotypeAndAssemblySequence
net.maizegenetics.pangenome.hapCalling.
SAMToMappingPluginKt
net.maizegenetics.pangenome.
GVCFStats
net.maizegenetics.pangenome.api.
HaplotypeGraphStreamBuilderPlugin
net.maizegenetics.pangenome.
ConvertToHaplotypeCallerInput
net.maizegenetics.pangenome.db_loading.
AddTaxaToTaxaGroupPluginKt
net.maizegenetics.pangenome.hapCalling.
HapIdMultiset
net.maizegenetics.pangenome.fastaExtraction.
ExtractFastaUtils
net.maizegenetics.pangenome.fastaExtraction.
CreateDBLoadScripts
net.maizegenetics.pangenome.db_loading.
GeneGFFData
net.maizegenetics.pangenome.gvcfFiltering.
ComputeMedianGVCFAndFilter
net.maizegenetics.pangenome.hapcollapse.
FindHaplotypeClustersPlugin
net.maizegenetics.pangenome.api.
ReferenceRangeEmissionProbability
net.maizegenetics.pangenome.io.
PathsToFastaPlugin
net.maizegenetics.pangenome.api.
MergeVariantInfosKt
net.maizegenetics.pangenome.db_loading.
VCFFile
net.maizegenetics.pangenome.hapCalling.
ConvertReadsToPathUsingHMM
net.maizegenetics.pangenome.hapcollapse.
RefAltData
net.maizegenetics.pangenome.api.
HaplotypeGraphBuilderPlugin
net.maizegenetics.pangenome.hapCalling.
ImportHaplotypePathFilePlugin
net.maizegenetics.pangenome.db_loading.
CloseDBConnectionPlugin
Interface Hierarchy
net.maizegenetics.pangenome.db_loading.
PHGData
net.maizegenetics.pangenome.db_loading.
PHGDataWriter
Enum Hierarchy
net.maizegenetics.pangenome.processAssemblyGenomes.
MAFToGVCFPlugin.OUTPUT_TYPE
net.maizegenetics.pangenome.hapcollapse.
ProfileMxdivPlugin.DistanceType
net.maizegenetics.pangenome.db_loading.
DBLoadingUtils.GenomeFileType
net.maizegenetics.pangenome.hapCalling.
ReadMappingInputFileFormat
net.maizegenetics.pangenome.hapcollapse.
FindHaplotypeClustersPlugin.CLUSTER_METHOD
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.ALGORITHM_TYPE
net.maizegenetics.pangenome.pipeline.
ImputePipelinePlugin.INPUT_TYPE
net.maizegenetics.pangenome.processAssemblyGenomes.
AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT
net.maizegenetics.pangenome.db_loading.
DBLoadingUtils.MethodType
net.maizegenetics.pangenome.pipeline.
ImputePipelinePlugin.IMPUTE_TASK
net.maizegenetics.pangenome.hapcollapse.
FillIndelsIntoConsensus.INDEL_MERGE_RULE
net.maizegenetics.pangenome.hapcollapse.
RunHapConsensusPipelinePlugin.CLUSTERING_MODE
net.maizegenetics.pangenome.hapcollapse.
DistanceCalculation
net.maizegenetics.pangenome.db_loading.
DBLoadingUtils.AnchorType
net.maizegenetics.pangenome.hapcollapse.
GVCFTyperPlugin.EMIT_MODE
net.maizegenetics.pangenome.hapCalling.
KmerMapType
net.maizegenetics.pangenome.pipeline.
PopulatePHGDBPipelinePlugin.ASSEMBLY_ALIGNER
net.maizegenetics.pangenome.api.
ReferenceRangeEmissionProbability.METHOD
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