net.maizegenetics.util

Class HDF5Utils

net.maizegenetics.util.HDF5Utils

public class HDF5Utils

Method Detail

isTASSEL4HDF5Format

public static boolean isTASSEL4HDF5Format(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

createHDF5TaxaModule

public static void createHDF5TaxaModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

lockHDF5TaxaModule

public static void lockHDF5TaxaModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

unlockHDF5TaxaModule

public static void unlockHDF5TaxaModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

doesTaxaModuleExist

public static boolean doesTaxaModuleExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

doTaxonCallsExist

public static boolean doTaxonCallsExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                        java.lang.String taxonName)

doTaxonCallsExist

public static boolean doTaxonCallsExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                        Taxon taxon)

isTaxaLocked

public static boolean isTaxaLocked(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

addTaxon

public static boolean addTaxon(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                               Taxon taxon)

Adds a taxon to the taxon module

Parameters:

h5w -

taxon -

Returns:

org.jetbrains.dokka.NodeRenderContent@7dc89a16: true if new add, false if already exists

writeHDF5Annotation

public static void writeHDF5Annotation(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                                       java.lang.String path,
                                       GeneralAnnotation annotations)

replaceTaxonAnnotations

public static void replaceTaxonAnnotations(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                           Taxon modifiedTaxon)

readHDF5Annotation

public static GeneralAnnotationStorage readHDF5Annotation(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                          java.lang.String path)

readHDF5Annotation

public static GeneralAnnotationStorage readHDF5Annotation(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                          java.lang.String path,
                                                          java.lang.String[] annotationKeys)

getTaxon

public static Taxon getTaxon(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                             java.lang.String taxonName)

getAllTaxaNames

public static java.util.List<java.lang.String> getAllTaxaNames(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

writeHDF5TaxaNumTaxa

public static void writeHDF5TaxaNumTaxa(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                        int numTaxa)

getHDF5TaxaNumTaxa

public static int getHDF5TaxaNumTaxa(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getHDF5GenotypeTaxaNumber

public static int getHDF5GenotypeTaxaNumber(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

createHDF5GenotypeModule

public static void createHDF5GenotypeModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

lockHDF5GenotypeModule

public static void lockHDF5GenotypeModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

unlockHDF5GenotypeModule

public static void unlockHDF5GenotypeModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

doesGenotypeModuleExist

public static boolean doesGenotypeModuleExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

isHDF5GenotypeLocked

public static boolean isHDF5GenotypeLocked(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

writeHDF5GenotypesMaxNumAlleles

public static void writeHDF5GenotypesMaxNumAlleles(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                                   int maxNumAlleles)

writeHDF5GenotypesRetainRareAlleles

public static void writeHDF5GenotypesRetainRareAlleles(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                                       boolean retainRareAlleles)

writeHDF5GenotypesNumTaxa

public static void writeHDF5GenotypesNumTaxa(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                             int numTaxa)

writeHDF5GenotypesScoreType

public static void writeHDF5GenotypesScoreType(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                               java.lang.String scoreType)

writeHDF5GenotypesAlleleStates

public static void writeHDF5GenotypesAlleleStates(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                                  java.lang.String[] aEncodings)

getHDF5GenotypesCalls

public static kotlin.Array[] getHDF5GenotypesCalls(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                   java.lang.String taxon)

writeHDF5GenotypesCalls

public static void writeHDF5GenotypesCalls(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                           java.lang.String taxon,
                                           kotlin.Array[] calls)

replaceHDF5GenotypesCalls

public static void replaceHDF5GenotypesCalls(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                             java.lang.String taxon,
                                             kotlin.Array[] calls)

replaceHDF5GenotypesCalls

public static void replaceHDF5GenotypesCalls(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                             java.lang.String taxon,
                                             int startSite,
                                             kotlin.Array[] calls)

getHDF5GenotypesDepth

public static kotlin.Array[] getHDF5GenotypesDepth(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                   java.lang.String taxon)

doesGenotypeDepthExist

public static boolean doesGenotypeDepthExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

writeHDF5GenotypesDepth

public static void writeHDF5GenotypesDepth(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                           java.lang.String taxon,
                                           kotlin.Array[] depth)

replaceHDF5GenotypesDepth

public static void replaceHDF5GenotypesDepth(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                             java.lang.String taxon,
                                             kotlin.Array[] depth)

getHDF5Alleles

public static kotlin.Array[] getHDF5Alleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                            WHICH_ALLELE allele)

getHDF5GenotypeSiteScores

public static kotlin.Array[] getHDF5GenotypeSiteScores(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                       java.lang.String taxon,
                                                       java.lang.String siteScoreType)

writeHDF5GenotypeSiteScores

public static void writeHDF5GenotypeSiteScores(ch.systemsx.cisd.hdf5.IHDF5Writer writer,
                                               java.lang.String taxon,
                                               java.lang.String siteScoreType,
                                               kotlin.Array[] values)

getHDF5PositionNumber

public static int getHDF5PositionNumber(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

createHDF5PositionModule

public static void createHDF5PositionModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w)

writeHDF5PositionNumSite

public static void writeHDF5PositionNumSite(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                            int numSites)

getHDF5ReferenceAlleles

public static kotlin.Array[] getHDF5ReferenceAlleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getHDF5ReferenceAlleles

public static kotlin.Array[] getHDF5ReferenceAlleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                     int startSite,
                                                     int numSites)

getHDF5AncestralAlleles

public static kotlin.Array[] getHDF5AncestralAlleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getHDF5AncestralAlleles

public static kotlin.Array[] getHDF5AncestralAlleles(ch.systemsx.cisd.hdf5.IHDF5Reader reader,
                                                     int startSite,
                                                     int numSites)

createHDF5TagModule

public static void createHDF5TagModule(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                       int tagLengthInLong)

isHDF5TagLocked

public static boolean isHDF5TagLocked(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getHDF5TagCount

public static int getHDF5TagCount(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getHDF5TagLengthInLong

public static int getHDF5TagLengthInLong(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

doTagsExist

public static boolean doTagsExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

getTagPath

public static java.lang.String getTagPath(Tag tag)

getTags

public static kotlin.Array[] getTags(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

writeTagDistributionBucket

public static void writeTagDistributionBucket(ch.systemsx.cisd.hdf5.IHDF5Writer h5w,
                                              int bucket,
                                              kotlin.Array[] tags,
                                              kotlin.Array[] length,
                                              kotlin.Array[] encodedTaxaDist,
                                              int maxTaxa,
                                              kotlin.Array[] tagDistOffset)

doTagsByTaxaExist

public static boolean doTagsByTaxaExist(ch.systemsx.cisd.hdf5.IHDF5Reader reader)

writeHDF5EntireArray

public static void writeHDF5EntireArray(java.lang.String objectPath,
                                        ch.systemsx.cisd.hdf5.IHDF5Writer myWriter,
                                        int objMaxLength,
                                        int blockSize,
                                        java.lang.Object val)

Parameters:

objectPath -

myWriter -

objMaxLength -

blockSize -

val -

writeHDF5Block

public static void writeHDF5Block(java.lang.String objectPath,
                                  ch.systemsx.cisd.hdf5.IHDF5Writer myWriter,
                                  int blockSize,
                                  int block,
                                  java.lang.Object val)

Parameters:

objectPath -

myWriter -

blockSize -

block -

val -