A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W
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.