Uses of Class
net.maizegenetics.dna.snp.score.ReferenceProbability

Packages that use ReferenceProbability

Package	Description
net.maizegenetics.dna.snp	Data structures for holding SNP and indel variation across taxa (samples) and genomic positions.
net.maizegenetics.dna.snp.score	Support for site scores (for example quality scores or imputation accuracy).

Uses of ReferenceProbability in net.maizegenetics.dna.snp

Methods in net.maizegenetics.dna.snp that return ReferenceProbability

Modifier and Type	Method and Description
ReferenceProbability	CombineGenotypeTable.referenceProbability()
ReferenceProbability	CoreGenotypeTable.referenceProbability()
ReferenceProbability	GenotypeTable.referenceProbability() Returns reference probability object (null if not present)
ReferenceProbability	MergedGenotypeTable.referenceProbability()
ReferenceProbability	TOPMGenotypeTable.referenceProbability()

Methods in net.maizegenetics.dna.snp with parameters of type ReferenceProbability

Modifier and Type	Method and Description
static GenotypeTable	GenotypeTableBuilder.getInstance(GenotypeCallTable genotype, PositionList positionList, TaxaList taxaList, AlleleDepth alleleDepth, AlleleProbability alleleProbability, ReferenceProbability referenceProbability, Dosage dosage, GeneralAnnotationStorage annotations) Standard approach for creating a new Alignment

Uses of ReferenceProbability in net.maizegenetics.dna.snp.score

Subclasses of ReferenceProbability in net.maizegenetics.dna.snp.score

Modifier and Type	Class and Description
class	FilterReferenceProbability
class	MaskReferenceProbability

Methods in net.maizegenetics.dna.snp.score that return ReferenceProbability

Modifier and Type	Method and Description
ReferenceProbability	ReferenceProbabilityBuilder.build()
static ReferenceProbability	ReferenceProbabilityBuilder.getFilteredInstance(ReferenceProbability base, Translate translate)
static ReferenceProbability	ReferenceProbabilityBuilder.getInstance(ch.systemsx.cisd.hdf5.IHDF5Reader reader)
static ReferenceProbability	ReferenceProbabilityBuilder.getMaskInstance(ReferenceProbability base, MaskMatrix mask)

Methods in net.maizegenetics.dna.snp.score with parameters of type ReferenceProbability

Modifier and Type	Method and Description
static ReferenceProbability	ReferenceProbabilityBuilder.getFilteredInstance(ReferenceProbability base, Translate translate)
static ReferenceProbability	ReferenceProbabilityBuilder.getMaskInstance(ReferenceProbability base, MaskMatrix mask)