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U

updateReadMappingHash() - function in net.maizegenetics.pangenome.db_loading.PHGDataWriter
This prompts a call to private method loadReadMappingHash() to update this hash table
updateReadMappingHash() - function in net.maizegenetics.pangenome.db_loading.PHGdbAccess
This prompts a call to private method loadReadMappingHash() to update this hash table
upgma - enum entry in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD
 
upgma - enum entry in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.CLUSTERING_MODE
 
upgma_assembly - enum entry in net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.CLUSTERING_MODE
 
upperPoissonBound() - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
Upper Poisson Bound used for filtering.
upperPoissonBound(Double) - function in net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
Set Upper Poisson Bound.
usageParameters() - function in net.maizegenetics.plugindef.AbstractPlugin
 
useBackwardForward() - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
Use the Backward-Forward algorithm instead of the Viterbi algorithm for the HMM.
useBackwardForward(Boolean) - function in net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
Set Usebf.
useDepthForCalls() - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
Boolean flag to have the clustering algorithm use depth information instead of allele counts
useDepthForCalls(Boolean) - function in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
Set Use Depth For Calls.
userid() - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
Userid for database
userid(String) - function in net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
Set Userid.
userid() - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
Userid for database
userid(String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
Set Userid.
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