Uses of Class
net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

Packages that use FindHaplotypeClustersPlugin

Package	Description
net.maizegenetics.pangenome.hapcollapse

Uses of FindHaplotypeClustersPlugin in net.maizegenetics.pangenome.hapcollapse

Methods in net.maizegenetics.pangenome.hapcollapse that return FindHaplotypeClustersPlugin

Modifier and Type	Method and Description
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.clusterMethod(FindHaplotypeClustersPlugin.CLUSTER_METHOD value) Set Cluster Method.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.intervalFile(String value) Set Interval File.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.maxDistFromFounder(Double value) Set Max divergence from founder.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.maxError(Double value) Set Maximum error.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.minSiteForComp(Integer value) Set Min sites to cluster.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.minTaxaCoverage(Double value) Set Min taxa coverage.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.minTaxaInGroup(Integer value) Set Min taxa to generate a haplotype.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.outFile(String value) Set Donor dir/file basename.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.referenceSequence(net.maizegenetics.dna.map.GenomeSequence value) Set Reference Genome Sequence.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.replaceNsWithMajor(Boolean value) Set Replace N calls with Major Allele.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.seqErrorRate(Double value) Set Sequencing error rate.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.sequenceOutDir(String value) Set Sequence Output Directory.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.useDepthForCalls(Boolean value) Set Use Depth For Calls.
FindHaplotypeClustersPlugin	FindHaplotypeClustersPlugin.vcfDir(String value) Set Target directory.