net.maizegenetics.dna.snp.genotypecall

Class GOBIIAvroGenotypeCallTable

net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable

public class GOBIIAvroGenotypeCallTable

Field Detail

GENOTYPE_BLOCK_SIZE

public static int GENOTYPE_BLOCK_SIZE

See Also:

Constant Field Values

myNumCacheMisses

public static int myNumCacheMisses

myNumBlocksRead

public static int myNumBlocksRead

myTimeReading

public static long myTimeReading

myNumProcesses

public static int myNumProcesses

Method Detail

getInstance

public static GOBIIAvroGenotypeCallTable getInstance(int numTaxa,
                                                     int numSites,
                                                     boolean phased,
                                                     org.apache.avro.generic.GenericRecord record)

getCacheKey

public static long getCacheKey(int taxon,
                               int site)

getKey

public static java.lang.String getKey(int taxon,
                                      int site)

genotype

public byte genotype(int taxon,
                     int site)

genotypeForAllTaxa

public kotlin.Array[] genotypeForAllTaxa(int site)

genotypeAllSites

public kotlin.Array[] genotypeAllSites(int taxon)

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()