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Hierarchy For Package net.maizegenetics.pangenome.hapCalling
Package Hierarchies:
All Packages
Class Hierarchy
net.maizegenetics.pangenome.hapCalling.
ImportDiploidPathPlugin
net.maizegenetics.pangenome.hapCalling.
DiploidTransitionProbabilityWithInbreeding
net.maizegenetics.pangenome.hapCalling.
MostLikelyParents
net.maizegenetics.pangenome.hapCalling.
MergeFastqPlugin
net.maizegenetics.pangenome.hapCalling.
PositionToRefAndAltHaplotypes
net.maizegenetics.pangenome.hapCalling.
PathsToVCFPlugin
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPluginKt
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPlugin.RefRangeStats
net.maizegenetics.pangenome.hapCalling.
HapIdStats
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPlugin
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaPlugin
net.maizegenetics.pangenome.hapCalling.
SNPToReadMappingPlugin
net.maizegenetics.pangenome.hapCalling.
KmerMap
net.maizegenetics.pangenome.hapCalling.
MutableKmerCounter
net.maizegenetics.pangenome.hapCalling.
MutableKmerToIdMap
net.maizegenetics.pangenome.hapCalling.
VerifyPathsPluginKt
net.maizegenetics.pangenome.hapCalling.
GraphIdMaps
net.maizegenetics.pangenome.hapCalling.
ScoreRangesByInclusionCountsPlugin
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypesBySNPPlugin
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin.PathFindingInput
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypeKmersPlugin
net.maizegenetics.pangenome.hapCalling.
SimulatedReadsPlugin
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaConverter
net.maizegenetics.pangenome.hapCalling.
PathToIgraphPlugin
net.maizegenetics.pangenome.hapCalling.
ExportVCForTaxonMethodPlugin
net.maizegenetics.pangenome.hapCalling.
ConvertRampSeqTagsToMapPlugin
net.maizegenetics.pangenome.hapCalling.
FastqToHapCountMinimapPluginKt
net.maizegenetics.pangenome.hapCalling.
ExportHaplotypePathToFilePlugin
net.maizegenetics.pangenome.hapCalling.
SingleHapMapping
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPlugin.AlignmentSummary
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPluginKt
net.maizegenetics.pangenome.hapCalling.
FastqDirToMappingPlugin
net.maizegenetics.pangenome.hapCalling.
IndexHaplotypesBySNPPluginKt
net.maizegenetics.pangenome.hapCalling.
HapCallingUtils
net.maizegenetics.pangenome.hapCalling.
DiploidTransitionProbability
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin.VCFSummary
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPlugin.ReadMappingResult
net.maizegenetics.pangenome.hapCalling.
RefRangeWrapper
net.maizegenetics.pangenome.hapCalling.
FastqToHapCountMinimapPlugin
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPlugin
net.maizegenetics.pangenome.hapCalling.
GraphIdMapsKt
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin
net.maizegenetics.pangenome.hapCalling.
HapCountBestPathToTextPlugin
net.maizegenetics.pangenome.hapCalling.
FastqDirToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin.IndelDistributions
net.maizegenetics.pangenome.hapCalling.
PathsToVCFHaplotypesPlugin
net.maizegenetics.pangenome.hapCalling.
VCFMetricsPlugin
net.maizegenetics.pangenome.hapCalling.
GetHapIdsForTaxonPlugin
net.maizegenetics.pangenome.hapCalling.
HapIdSetCount
net.maizegenetics.pangenome.hapCalling.
DiploidEmissionProbability
net.maizegenetics.pangenome.hapCalling.
SAMToMappingPlugin
net.maizegenetics.pangenome.hapCalling.
KmerUtils
net.maizegenetics.pangenome.hapCalling.
IndexKmerByHammingPlugin
net.maizegenetics.pangenome.hapCalling.
FastqToKmerCountPlugin
net.maizegenetics.pangenome.hapCalling.
FilterFastqUsingBAMPlugin
net.maizegenetics.pangenome.hapCalling.
CreateHapIdMapsPlugin
net.maizegenetics.pangenome.hapCalling.
SplitKeyFilePlugin
net.maizegenetics.pangenome.hapCalling.
Minimap2Utils
net.maizegenetics.pangenome.hapCalling.
SNPToReadMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
FastqcolToFastaPluginKt
net.maizegenetics.pangenome.hapCalling.
ReadMappingDecoder
net.maizegenetics.pangenome.hapCalling.
MultisampleBAMToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
DiploidCountsToPath
net.maizegenetics.pangenome.hapCalling.
FindBestDiploidPathKt
net.maizegenetics.pangenome.hapCalling.
ReadMappingKeyFileParsed
net.maizegenetics.pangenome.hapCalling.
SecondaryStats
net.maizegenetics.pangenome.hapCalling.
LikelyParentsPlugin
net.maizegenetics.pangenome.hapCalling.
FastqToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
KeyFileUniqueRecord
net.maizegenetics.pangenome.hapCalling.
SplitKeyFilePluginKt
net.maizegenetics.pangenome.hapCalling.
ImportReadMappingToDBPlugin
net.maizegenetics.pangenome.hapCalling.
MergeFastqPluginKt
net.maizegenetics.pangenome.hapCalling.
KmerToRefRangeIdToPurgeArray
net.maizegenetics.pangenome.hapCalling.
BestAlignmentGroup
net.maizegenetics.pangenome.hapCalling.
FastqToMappingPlugin
net.maizegenetics.pangenome.hapCalling.
ImportReadMappingToDBPluginKt
net.maizegenetics.pangenome.hapCalling.
ReadMappingUtils
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.PathFindingInput
net.maizegenetics.pangenome.hapCalling.
ViterbiForDiploidPath
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPluginKt
net.maizegenetics.pangenome.hapCalling.
PathFinderForSingleTaxonNodes
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.PathFindingResult
net.maizegenetics.pangenome.hapCalling.
SAMToMappingPluginKt
net.maizegenetics.pangenome.hapCalling.
PathFinderForSingleTaxonNodesFactory
net.maizegenetics.pangenome.hapCalling.
SAMMetricsPlugin
net.maizegenetics.pangenome.hapCalling.
FilterBAMAndGetStatsPluginKt
net.maizegenetics.pangenome.hapCalling.
HapIdMultiset
net.maizegenetics.pangenome.hapCalling.
DiploidPathPlugin.PathFindingResult
net.maizegenetics.pangenome.hapCalling.
HapCountBestPathPlugin
net.maizegenetics.pangenome.hapCalling.
CreateHapIdMapsPluginKt
net.maizegenetics.pangenome.hapCalling.
ConvertReadsToPathUsingHMM
net.maizegenetics.pangenome.hapCalling.
VerifyPathsPlugin
net.maizegenetics.pangenome.hapCalling.
ImportHaplotypePathFilePlugin
Enum Hierarchy
net.maizegenetics.pangenome.hapCalling.
KmerMapType
net.maizegenetics.pangenome.hapCalling.
ReadMappingInputFileFormat
net.maizegenetics.pangenome.hapCalling.
BestHaplotypePathPlugin.ALGORITHM_TYPE
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