net.maizegenetics.dna.snp.genotypecall

Class LineIndexHapmapGenotypeCallTable

net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable

public class LineIndexHapmapGenotypeCallTable

Method Detail

getInstance

public static LineIndexHapmapGenotypeCallTable getInstance(int numTaxa,
                                                           int numSites,
                                                           boolean phased,
                                                           boolean isOneLetter,
                                                           LineIndex index,
                                                           java.lang.String filename)

genotype

public byte genotype(int taxon,
                     int site)

genotypeForAllTaxa

public kotlin.Array[] genotypeForAllTaxa(int site)

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()