net.maizegenetics.util

Class Tassel5HDF5Constants

net.maizegenetics.util.Tassel5HDF5Constants

public class Tassel5HDF5Constants

Definition of attributes and paths for Tassel HDF5 file format.

Field Detail

ROOT

public static java.lang.String ROOT

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Constant Field Values

GENOTYPES_MODULE

public static java.lang.String GENOTYPES_MODULE

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Constant Field Values

GENOTYPES_ATTRIBUTES_PATH

public static java.lang.String GENOTYPES_ATTRIBUTES_PATH

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Constant Field Values

GENOTYPES_MAX_NUM_ALLELES

public static java.lang.String GENOTYPES_MAX_NUM_ALLELES

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Constant Field Values

GENOTYPES_RETAIN_RARE_ALLELES

public static java.lang.String GENOTYPES_RETAIN_RARE_ALLELES

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Constant Field Values

GENOTYPES_NUM_TAXA

public static java.lang.String GENOTYPES_NUM_TAXA

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Constant Field Values

GENOTYPES_LOCKED

public static java.lang.String GENOTYPES_LOCKED

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Constant Field Values

GENOTYPES_SCORE_TYPE

public static java.lang.String GENOTYPES_SCORE_TYPE

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Constant Field Values

GENOTYPES_ALLELE_STATES

public static java.lang.String GENOTYPES_ALLELE_STATES

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Constant Field Values

GENO_DESC

public static java.lang.String GENO_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

ALLELE_FREQ_ORD

public static java.lang.String ALLELE_FREQ_ORD

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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

BLOCK_SIZE

public static int BLOCK_SIZE

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Constant Field Values

TAXA_MODULE

public static java.lang.String TAXA_MODULE

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Constant Field Values

TAXA_ATTRIBUTES_PATH

public static java.lang.String TAXA_ATTRIBUTES_PATH

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Constant Field Values

TAXA_NUM_TAXA

public static java.lang.String TAXA_NUM_TAXA

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Constant Field Values

TAXA_LOCKED

public static java.lang.String TAXA_LOCKED

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Constant Field Values

TAXA_ORDER

public static java.lang.String TAXA_ORDER

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Constant Field Values

POSITION_MODULE

public static java.lang.String POSITION_MODULE

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Constant Field Values

POSITION_ATTRIBUTES_PATH

public static java.lang.String POSITION_ATTRIBUTES_PATH

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Constant Field Values

POSITION_NUM_SITES

public static java.lang.String POSITION_NUM_SITES

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Constant Field Values

POSITION_HAS_REFEFERENCE

public static java.lang.String POSITION_HAS_REFEFERENCE

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Constant Field Values

POSITION_GENOME_VERSION

public static java.lang.String POSITION_GENOME_VERSION

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Constant Field Values

POSITIONS

public static java.lang.String POSITIONS

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Constant Field Values

CHROMOSOMES

public static java.lang.String CHROMOSOMES

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Constant Field Values

CHROMOSOME_INDICES

public static java.lang.String CHROMOSOME_INDICES

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Constant Field Values

SNP_IDS

public static java.lang.String SNP_IDS

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Constant Field Values

REF_ALLELES

public static java.lang.String REF_ALLELES

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Constant Field Values

ANC_ALLELES

public static java.lang.String ANC_ALLELES

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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

TAG_MODULE

public static java.lang.String TAG_MODULE

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Constant Field Values

TAG_ATTRIBUTES_PATH

public static java.lang.String TAG_ATTRIBUTES_PATH

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Constant Field Values

TAG_COUNT

public static java.lang.String TAG_COUNT

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Constant Field Values

TAG_LENGTH_LONG

public static java.lang.String TAG_LENGTH_LONG

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Constant Field Values

TAG_LOCKED

public static java.lang.String TAG_LOCKED

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Constant Field Values

TAGS

public static java.lang.String TAGS

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Constant Field Values

TAGS_BIN_NUM

public static int TAGS_BIN_NUM

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Constant Field Values

HASH_SHIFT_TO_TAG_BIN

public static int HASH_SHIFT_TO_TAG_BIN

TAG_SEQ

public static java.lang.String TAG_SEQ

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Constant Field Values

TAG_LENGTHS

public static java.lang.String TAG_LENGTHS

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Constant Field Values

TAG_DIST

public static java.lang.String TAG_DIST

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Constant Field Values

TAG_DIST_OFFSETS

public static java.lang.String TAG_DIST_OFFSETS

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Constant Field Values

Method Detail

getGenotypesPedigreePath

public static java.lang.String getGenotypesPedigreePath(java.lang.String taxon)

getGenotypesCallsPath

public static java.lang.String getGenotypesCallsPath(java.lang.String taxon)

getGenotypesDepthPath

public static java.lang.String getGenotypesDepthPath(java.lang.String taxon)

Deprecated.

getGenotypesSiteScorePath

public static java.lang.String getGenotypesSiteScorePath(java.lang.String taxon,
                                                         java.lang.String siteScoreType)

getTaxonPath

public static java.lang.String getTaxonPath(java.lang.String taxon)