net.maizegenetics.dna.snp

Class HapMapHDF5Constants

net.maizegenetics.dna.snp.HapMapHDF5Constants

public class HapMapHDF5Constants

Definition of fields and directories of the GenotypeTable in a HDF5 file format.

Field Detail

ROOT

public static java.lang.String ROOT

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Constant Field Values

TAXA

public static java.lang.String TAXA

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Constant Field Values

ALLELE_STATES

public static java.lang.String ALLELE_STATES

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Constant Field Values

POSITIONS

public static java.lang.String POSITIONS

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Constant Field Values

ALLELES

public static java.lang.String ALLELES

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Constant Field Values

TBIT

public static java.lang.String TBIT

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Constant Field Values

SBIT

public static java.lang.String SBIT

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Constant Field Values

DEPTH

public static java.lang.String DEPTH

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Constant Field Values

GENOTYPES

public static java.lang.String GENOTYPES

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Constant Field Values

LOCI

public static java.lang.String LOCI

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Constant Field Values

LOCUS_OFFSETS

public static java.lang.String LOCUS_OFFSETS

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Constant Field Values

LOCUS_INDICES

public static java.lang.String LOCUS_INDICES

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Constant Field Values

SNP_IDS

public static java.lang.String SNP_IDS

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Constant Field Values

SITE_DESC

public static java.lang.String SITE_DESC

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Constant Field Values

ALLELE_CNT

public static java.lang.String ALLELE_CNT

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Constant Field Values

MAF

public static java.lang.String MAF

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Constant Field Values

SITECOV

public static java.lang.String SITECOV

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Constant Field Values

SITEHET

public static java.lang.String SITEHET

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Constant Field Values

MAJOR_ALLELE

public static java.lang.String MAJOR_ALLELE

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Constant Field Values

MINOR_ALLELE

public static java.lang.String MINOR_ALLELE

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Constant Field Values

ALLELE_FREQ_ORD

public static java.lang.String ALLELE_FREQ_ORD

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Constant Field Values

REF_ALLELE

public static java.lang.String REF_ALLELE

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Constant Field Values

TAXA_DESC

public static java.lang.String TAXA_DESC

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Constant Field Values

TAXACOV

public static java.lang.String TAXACOV

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Constant Field Values

TAXAHET

public static java.lang.String TAXAHET

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Constant Field Values

LD_DESC

public static java.lang.String LD_DESC

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Constant Field Values

LDR2_DESC

public static java.lang.String LDR2_DESC

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Constant Field Values

LDP_DESC

public static java.lang.String LDP_DESC

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Constant Field Values

LDPropLD_DESC

public static java.lang.String LDPropLD_DESC

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Constant Field Values

LDMinDist_DESC

public static java.lang.String LDMinDist_DESC

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Constant Field Values

BPLDMean34

public static java.lang.String BPLDMean34

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Constant Field Values

BPLDMeanMax

public static java.lang.String BPLDMeanMax

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Constant Field Values

BPmaxMaxLD

public static java.lang.String BPmaxMaxLD

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Constant Field Values

BPminMaxLD

public static java.lang.String BPminMaxLD

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Constant Field Values

BPPopCnt

public static java.lang.String BPPopCnt

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Constant Field Values

ERROR_DESC

public static java.lang.String ERROR_DESC

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Constant Field Values

BPECERROR_DESC

public static java.lang.String BPECERROR_DESC

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Constant Field Values

BPECAVGR2_DESC

public static java.lang.String BPECAVGR2_DESC

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Constant Field Values

IBSERRORRATE_DESC

public static java.lang.String IBSERRORRATE_DESC

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Constant Field Values

IBSMINORERRORRATE_DESC

public static java.lang.String IBSMINORERRORRATE_DESC

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Constant Field Values

IBSERROR_DESC

public static java.lang.String IBSERROR_DESC

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Constant Field Values

IBSMINORCORR_DESC

public static java.lang.String IBSMINORCORR_DESC

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Constant Field Values

IBSMAJORCORR_DESC

public static java.lang.String IBSMAJORCORR_DESC

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Constant Field Values

DEFAULT_ATTRIBUTES_PATH

public static java.lang.String DEFAULT_ATTRIBUTES_PATH

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Constant Field Values

NUM_SBIT_WORDS

public static java.lang.String NUM_SBIT_WORDS

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Constant Field Values

NUM_TBIT_WORDS

public static java.lang.String NUM_TBIT_WORDS

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Constant Field Values

NUM_TAXA

public static java.lang.String NUM_TAXA

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Constant Field Values

NUM_SITES

public static java.lang.String NUM_SITES

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Constant Field Values

BLOCK_SIZE

public static java.lang.String BLOCK_SIZE

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Constant Field Values

MAX_NUM_ALLELES

public static java.lang.String MAX_NUM_ALLELES

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Constant Field Values

RETAIN_RARE_ALLELES

public static java.lang.String RETAIN_RARE_ALLELES

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Constant Field Values

NUM_LD_BINS

public static java.lang.String NUM_LD_BINS

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Constant Field Values

LD_BINS

public static java.lang.String LD_BINS

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Constant Field Values

intDeflation

public static ch.systemsx.cisd.hdf5.HDF5IntStorageFeatures intDeflation

genDeflation

public static ch.systemsx.cisd.hdf5.HDF5GenericStorageFeatures genDeflation

floatDeflation

public static ch.systemsx.cisd.hdf5.HDF5FloatStorageFeatures floatDeflation

GWAS

public static java.lang.String GWAS

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Constant Field Values

GENOMIC

public static java.lang.String GENOMIC

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Constant Field Values

POP_GEN

public static java.lang.String POP_GEN

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Constant Field Values