net.maizegenetics.dna.snp.score

Class HDF5AlleleDepthBuilder

AlleleDepthBuilder

net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder

public class HDF5AlleleDepthBuilder
extends AlleleDepthBuilder

Builder to store information on DNA read depths.

Method Detail

getHDF5NucleotideInstance

public static HDF5AlleleDepthBuilder getHDF5NucleotideInstance(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@38f11f15:

getExistingHDF5Instance

public static AlleleDepth getExistingHDF5Instance(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

AlleleDepth is returned for an immutable HDF5 file

Parameters:

reader -

Returns:

org.jetbrains.dokka.NodeRenderContent@e832c70: allele depths

addTaxon

public HDF5AlleleDepthBuilder addTaxon(Taxon taxon,
                                       kotlin.Array[] depths)

Add taxon and set values for all sites and alleles for that taxon. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.

Parameters:

taxon - taxon

depths - depth values

Returns:

org.jetbrains.dokka.NodeRenderContent@14d09062: builder

addTaxon

public HDF5AlleleDepthBuilder addTaxon(Taxon taxon,
                                       kotlin.Array[] depths)

Add taxon and set values for all sites and alleles for that taxon. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.

Parameters:

taxon - taxon

depths - depth values

Returns:

org.jetbrains.dokka.NodeRenderContent@2acd4ec1: builder

build

public AlleleDepth build()