net.maizegenetics.dna.snp.genotypecall

Class ProjectionGenotypeCallTable

net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable

public class ProjectionGenotypeCallTable

Projection genotype use defined haplotypes and breakpoints that point to a high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.

The alignment built by this builder is a CoreGenotypeTable with a ProjectionGenotypeCallTable. The taxa indices come from the projection alignment file, while the site indices are the same as the base GenotypeTable. TODO this implement a projection interface with the getDonorHaplotypes method

Constructor Detail

ProjectionGenotypeCallTable

public ProjectionGenotypeCallTable(GenotypeTable hdAlign,
                                   com.google.common.collect.ImmutableList<java.util.NavigableSet> allBreakPoints)

Method Detail

getDonorHaplotypes

public java.util.NavigableSet<net.maizegenetics.dna.map.DonorHaplotypes> getDonorHaplotypes(int taxon)

genotype

public byte genotype(int taxon,
                     int site)

taxonDonors

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

getBaseGenotypeTable

public GenotypeTable getBaseGenotypeTable()

Returns the high density base genotypeTable of the projection genotypeTable.

Returns:

org.jetbrains.dokka.NodeRenderContent@8f201ad: base GenotypeTable

genotypeAsString

public java.lang.String genotypeAsString(int taxon,
                                         int site)

diploidAsString

public java.lang.String diploidAsString(int site,
                                        byte value)

transposeData

public void transposeData(boolean siteInnerLoop)

isSiteOptimized

public boolean isSiteOptimized()