net.maizegenetics.dna.snp.score

Class HDF5AlleleDepth

AlleleDepth

net.maizegenetics.dna.snp.score.HDF5AlleleDepth

All Implemented Interfaces:

SiteScore

public class HDF5AlleleDepth
extends AlleleDepth

Method Detail

valuesByte

public kotlin.Array[] valuesByte(int taxon,
                                 int site)

Returns the depth values (byte representation) of all nucleotides at given taxon and site. Depth values are stored in bytes and translated to integer using AlleleDepthUtil.depthByteToInt().

Parameters:

taxon - taxon

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@7819c8ab: depths

valuesForTaxonByte

public kotlin.Array[] valuesForTaxonByte(int taxon)

Returns depth values (byte representation) of all nucleotides and sites for given taxon. The first dimension of returned array is nucleotides (ALLELE_DEPTH_TYPES) and second dimension is sites.

Parameters:

taxon - taxon

Returns:

org.jetbrains.dokka.NodeRenderContent@608357dc: depths

value

public int value(int taxon,
                 int site,
                 net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE scoreType)

Returns the depth of nucleotide (scoreType) at given taxon and site. Depth values are stored in bytes and translated to integer using AlleleDepthUtil.depthByteToInt().

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

Returns:

org.jetbrains.dokka.NodeRenderContent@5159eac9: depth

values

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

Returns the depth values of all nucleotides at given taxon and site. Depth values are stored in bytes and translated to integer using AlleleDepthUtil.depthByteToInt().

Parameters:

taxon - taxon

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@1c98e7c6: depths

valueByte

public byte valueByte(int taxon,
                      int site,
                      net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE scoreType)

Returns the depth (byte representation) of nucleotide (scoreType) at given taxon and site. Depth values are stored in bytes and translated to integer using AlleleDepthUtil.depthByteToInt().

Parameters:

taxon - taxon

site - site

scoreType - nucleotide

Returns:

org.jetbrains.dokka.NodeRenderContent@2af2286e: depth