net.maizegenetics.dna.snp.genotypecall

Class AlleleFreqCache

net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache

public class AlleleFreqCache

Cache for allele frequency statistics. Allele frequency can be expensive to recalculate at large scale, so these class efficiently loops through blocks of sites and caches the statistics on them.

Field Detail

SITE_BLOCK_MASK

public static int SITE_BLOCK_MASK

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Constant Field Values

UNKNOWN_COUNT

public static int UNKNOWN_COUNT

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Constant Field Values

UNKNOWN_GAMETE_COUNT

public static int UNKNOWN_GAMETE_COUNT

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Constant Field Values

HETEROZYGOUS_COUNT

public static int HETEROZYGOUS_COUNT

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Constant Field Values

HOMOZYGOUS_COUNT

public static int HOMOZYGOUS_COUNT

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Constant Field Values

Constructor Detail

AlleleFreqCache

public AlleleFreqCache(GenotypeCallTable genotype,
                       int maxNumAlleles)

Method Detail

getAllelesSortedByFrequency

public kotlin.Array[] getAllelesSortedByFrequency(int site)

allelesSortedByFrequencyNucleotide

public static kotlin.Array[] allelesSortedByFrequencyNucleotide(kotlin.Array[] data)

allelesSortedByFrequencyAndCountsNucleotide

public static Stats allelesSortedByFrequencyAndCountsNucleotide(int index,
                                                                kotlin.Array[] data)

majorAllele

public static byte majorAllele(kotlin.Array[] alleles)

majorAlleleFrequency

public static double majorAlleleFrequency(kotlin.Array[] alleles)

minorAllele

public static byte minorAllele(kotlin.Array[] alleles)

minorAlleleFrequency

public static double minorAlleleFrequency(kotlin.Array[] alleles)

totalGametesNonMissingForSite

public static int totalGametesNonMissingForSite(kotlin.Array[] alleles)

proportionHeterozygous

public static double proportionHeterozygous(kotlin.Array[] counts,
                                            int totalCount)

proportionHeterozygous

public static double proportionHeterozygous(kotlin.Array[] data)