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Deprecated Classes
Class and Description
net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
Deprecated Methods
Method and Description
net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils.exportMergedRegions(mergedCoords, fileName)
net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils.mergeCoords(coordFile, chromosome)
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