net.maizegenetics.dna.snp.genotypecall

Class GenotypeCallTableBuilder

net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder

public class GenotypeCallTableBuilder

Builder to construct a GenotypeCallTable. This builder is generally only used in complex situations, where the GenotypeTableBuilder does not suffice.

Method Detail

getInstance

public static GenotypeCallTableBuilder getInstance(int numTaxa,
                                                   int numSites)

Get Genotype Builder given number of taxa and sites. Performance optimized for site loop inside taxon loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.

Parameters:

numTaxa - number of taxa

numSites - number of sites.

Returns:

org.jetbrains.dokka.NodeRenderContent@2b5dcd77: Genotype Builder

getInstanceTranspose

public static GenotypeCallTableBuilder getInstanceTranspose(int numTaxa,
                                                            int numSites)

Get Genotype Builder given number of taxa and sites. Performance optimized for taxon loop inside site loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.

Parameters:

numTaxa - number of taxa

numSites - number of sites.

Returns:

org.jetbrains.dokka.NodeRenderContent@db985a1: Genotype Builder

getUnphasedNucleotideGenotypeBuilder

public static GenotypeCallTableBuilder getUnphasedNucleotideGenotypeBuilder(int numTaxa,
                                                                            int numSites)

Get Genotype Builder given number of taxa and sites. Performance optimized for site loop inside taxon loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.

Parameters:

numTaxa - number of taxa

numSites - number of sites.

Returns:

org.jetbrains.dokka.NodeRenderContent@2ab6ad4b: Genotype Builder

getFilteredInstance

public static Tuple<net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable,net.maizegenetics.dna.snp.Translate> getFilteredInstance(GenotypeCallTable genotype,
                                                                                                                                      Translate translate)

getInstanceCopy

public static GenotypeCallTableBuilder getInstanceCopy(GenotypeCallTable genotype)

setBase

public GenotypeCallTableBuilder setBase(int taxon,
                                        int site,
                                        byte value)

setBaseRangeForTaxon

public GenotypeCallTableBuilder setBaseRangeForTaxon(int taxon,
                                                     int startSite,
                                                     kotlin.Array[] value)

setBases

public GenotypeCallTableBuilder setBases(java.lang.String[] data)

setBases

public GenotypeCallTableBuilder setBases(java.lang.String[] data)

isPhased

public GenotypeCallTableBuilder isPhased(boolean isPhased)

alleleEncodings

public GenotypeCallTableBuilder alleleEncodings(java.lang.String[] alleleEncodings)

getTaxaCount

public int getTaxaCount()

getSiteCount

public int getSiteCount()

reorderTaxa

public void reorderTaxa(kotlin.Array[] newIndices)

reorderPositions

public void reorderPositions(kotlin.Array[] newIndices)

build

public GenotypeCallTable build()

buildHDF5

public static GenotypeCallTable buildHDF5(java.lang.String filename)

buildHDF5

public static GenotypeCallTable buildHDF5(ch.systemsx.cisd.hdf5.IHDF5Reader reader)