net.maizegenetics.dna.snp

Class MaskMatrixBuilder

net.maizegenetics.dna.snp.MaskMatrixBuilder

public class MaskMatrixBuilder

Method Detail

getInstance

public static MaskMatrixBuilder getInstance(int numTaxa,
                                            int numSites,
                                            boolean isSiteOptimized)

getInstance

public static MaskMatrixBuilder getInstance(MaskMatrix orig)

getInstanceRemoveMinorSNPs

public static MaskMatrix getInstanceRemoveMinorSNPs(GenotypeCallTable genotype)

getInstanceRemoveHeterozygous

public static MaskMatrix getInstanceRemoveHeterozygous(GenotypeCallTable genotype)

getInstanceRemoveHomozygous

public static MaskMatrix getInstanceRemoveHomozygous(GenotypeCallTable genotype)

getInstanceRemoveIndels

public static MaskMatrix getInstanceRemoveIndels(GenotypeCallTable genotype)

getInstance

public static MaskMatrix getInstance(GenotypeCallTable genotype,
                                     java.util.function.Predicate<java.lang.Byte> predicate)

getInstance

public static MaskMatrix getInstance(GenotypeCallTable genotype,
                                     java.util.function.BiPredicate<java.lang.Byte,net.maizegenetics.dna.snp.genotypecall.Stats> predicate)

get

public boolean get(int taxon,
                   int site)

set

public void set(int taxon,
                int site)

setNext

public void setNext(boolean value)

reduceMaskTo

public long reduceMaskTo(double percent)

build

public MaskMatrix build()