net.maizegenetics.dna.snp.score

Class AlleleDepthBuilder

net.maizegenetics.dna.snp.score.AlleleDepthBuilder

Direct Known Subclasses:

HDF5AlleleDepthBuilder

public class AlleleDepthBuilder

Constructor Detail

AlleleDepthBuilder

protected AlleleDepthBuilder(int numSites)

Method Detail

getInstance

public static AlleleDepthBuilder getInstance(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                                             int numSites)

AlleleDepthBuilder is created and depths are stored in a HDF5 file. setDepth methods are used to set the depths. Finish the building with build()

Parameters:

writer -

numSites -

Returns:

org.jetbrains.dokka.NodeRenderContent@79eda470:

getFilteredInstance

public static AlleleDepth getFilteredInstance(HDF5AlleleDepth alleleDepth,
                                              FilterGenotypeTable filter)

getInstance

public static AlleleDepthBuilder getInstance(int numTaxa,
                                             int numSites,
                                             TaxaList taxaList)

This returns an AlleleDepthBuilder where depths are stored in memory.

Parameters:

numTaxa - number of taxa

numSites - number of sites

taxaList - taxa list

Returns:

org.jetbrains.dokka.NodeRenderContent@512b70b: AlleleDepthBuilder

getFilteredInstance

public static AlleleDepth getFilteredInstance(AlleleDepth base,
                                              Translate translate)

This creates a filtered AlleleDepth.

Parameters:

base - original AlleleDepth

translate - translate

Returns:

org.jetbrains.dokka.NodeRenderContent@ac7e5c: filtered AlleleDepth

getMaskInstance

public static AlleleDepth getMaskInstance(AlleleDepth base,
                                          MaskMatrix mask)

getInstance

public static AlleleDepth getInstance(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

This creates an AlleleDepth instance from an existing HDF5 file.

Parameters:

reader - reader

Returns:

org.jetbrains.dokka.NodeRenderContent@3ffc7b05: AlleleDepth

addTaxon

public AlleleDepthBuilder addTaxon(int taxon,
                                   kotlin.Array[] values,
                                   net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE type)

addTaxon

public AlleleDepthBuilder addTaxon(int taxon,
                                   kotlin.Array[] values)

setDepthRangeForTaxon

public AlleleDepthBuilder setDepthRangeForTaxon(int taxon,
                                                int siteOffset,
                                                kotlin.Array[] depths)

Set depth for range of sites and alleles for a taxon simultaneously. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.

Parameters:

taxon - Index of taxon

siteOffset - site offset

depths - array[allele][site] of all values

Returns:

org.jetbrains.dokka.NodeRenderContent@2b2696ae: builder

reorderPositions

public void reorderPositions(kotlin.Array[] newIndices)

build

public AlleleDepth build()