Uses of Class
net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs

Packages that use ConvertGBSToSNPs

Package	Description
net.maizegenetics.pangenome.hapCalling

Uses of ConvertGBSToSNPs in net.maizegenetics.pangenome.hapCalling

Methods in net.maizegenetics.pangenome.hapCalling that return ConvertGBSToSNPs

Modifier and Type	Method and Description
ConvertGBSToSNPs	ConvertGBSToSNPs.countHaplotypeNodesFromFastQ()
ConvertGBSToSNPs	ConvertGBSToSNPs.emissionProbabilityMethod(ReferenceRangeEmissionProbability.METHOD method)
ConvertGBSToSNPs	ConvertGBSToSNPs.filterHaplotypeGraph(HaplotypeGraph hapGraph) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
ConvertGBSToSNPs	ConvertGBSToSNPs.filterHaplotypeGraph(HaplotypeGraph hapGraph, List<Integer> rangesToKeep) This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.
ConvertGBSToSNPs	ConvertGBSToSNPs.hapidCountMap(Map<Integer,Integer> countmap)
ConvertGBSToSNPs	ConvertGBSToSNPs.hapidCounts(com.google.common.collect.Multiset<Integer> hapidCounts)
ConvertGBSToSNPs	ConvertGBSToSNPs.hapidExclusionCountMap(Map<Integer,Integer> countmap)
ConvertGBSToSNPs	ConvertGBSToSNPs.maxNodesPerRange(int maxNodes)
ConvertGBSToSNPs	ConvertGBSToSNPs.maxReadsPerRangeKB(int maxReads)
ConvertGBSToSNPs	ConvertGBSToSNPs.minReadsPerRange(int minReads)
ConvertGBSToSNPs	ConvertGBSToSNPs.minTaxaPerRange(int minTaxa)
ConvertGBSToSNPs	ConvertGBSToSNPs.minTransitionProbability(double minprob)
ConvertGBSToSNPs	ConvertGBSToSNPs.probabilityReadMappingCorrect(double probCorrect)
ConvertGBSToSNPs	ConvertGBSToSNPs.splitTaxa(boolean split)
ConvertGBSToSNPs	ConvertGBSToSNPs.targetTaxon(String taxonName)
ConvertGBSToSNPs	ConvertGBSToSNPs.taxaFilterList(String taxaNames)
ConvertGBSToSNPs	ConvertGBSToSNPs.taxaFilterList(net.maizegenetics.taxa.TaxaList listOfTaxa)
ConvertGBSToSNPs	ConvertGBSToSNPs.transitionProbabilitySameTaxon(double p)