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A

ALT - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

B

BATCH_SIZE - Static variable in class org.molgenis.data.vcf.VcfRepository

C

canImport(File, RepositoryCollection) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

CHROM - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

count() - Method in class org.molgenis.data.vcf.VcfRepository

createId(Entity) - Static method in class org.molgenis.data.vcf.utils.VcfUtils

Creates a internal molgenis id from a vcf entity

D

DEFAULT_ATTRIBUTE_DESCRIPTION - Static variable in class org.molgenis.data.vcf.VcfRepository

determineImportableEntities(MetaDataService, RepositoryCollection, String) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

doImport(RepositoryCollection, MetadataAction, DataAction, String) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

F

FILTER - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

forEachBatched(Consumer<List<Entity>>, int) - Method in class org.molgenis.data.vcf.VcfRepository

FORMAT_GT - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

G

getAltAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getCapabilities() - Method in class org.molgenis.data.vcf.VcfRepository

getChromAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getEntityType() - Method in class org.molgenis.data.vcf.format.VcfToEntity

getEntityType() - Method in class org.molgenis.data.vcf.VcfRepository

getEntityTypeIds() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getFilterAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getIdAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getMetadataAction(RepositoryCollection) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getMustChangeEntityName() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getName() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getOrder() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getPosAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getQualAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getRefAttribute() - Method in class org.molgenis.data.vcf.model.VcfAttributes

getRepository(String) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

getSupportedDataActions() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getSupportedFileExtensions() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getSupportedMetadataActions() - Method in class org.molgenis.data.vcf.importer.VcfImporterService

getVCF() - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

H

hasRepository(String) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

hasRepository(EntityType) - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

I

ID - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

INFO - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

init() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

INTERNAL_ID - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

iterator() - Method in class org.molgenis.data.vcf.VcfRepository

iterator() - Method in class org.molgenis.data.vcf.VcfRepositoryCollection

N

NAME - Static variable in class org.molgenis.data.vcf.VcfRepository

NAME - Static variable in class org.molgenis.data.vcf.VcfRepositoryCollection

O

org.molgenis.data.vcf - package org.molgenis.data.vcf

org.molgenis.data.vcf.format - package org.molgenis.data.vcf.format

org.molgenis.data.vcf.importer - package org.molgenis.data.vcf.importer

org.molgenis.data.vcf.model - package org.molgenis.data.vcf.model

org.molgenis.data.vcf.utils - package org.molgenis.data.vcf.utils

ORIGINAL_NAME - Static variable in class org.molgenis.data.vcf.VcfRepository

P

POS - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

Q

QUAL - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

R

REF - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

registerVcfRepositorySource() - Method in class org.molgenis.data.vcf.VcfDataConfig

Registers the VcfRepositorySource factory so it can be used by DataService.createFileRepositorySource(File file);

S

SAMPLES - Static variable in class org.molgenis.data.vcf.model.VcfAttributes

T

toEntity(VcfRecord) - Method in class org.molgenis.data.vcf.format.VcfToEntity

toString() - Method in enum org.molgenis.data.vcf.VcfFileExtensions

V

validateImport(RepositoryCollection) - Method in class org.molgenis.data.vcf.importer.VcfImporterService

valueOf(String) - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.data.vcf.VcfFileExtensions

Returns an array containing the constants of this enum type, in the order they are declared.

VCF - org.molgenis.data.vcf.VcfFileExtensions

VCF_GZ - org.molgenis.data.vcf.VcfFileExtensions

VCF_ZIP - org.molgenis.data.vcf.VcfFileExtensions

VcfAttributes - Class in org.molgenis.data.vcf.model

VcfAttributes(AttributeFactory) - Constructor for class org.molgenis.data.vcf.model.VcfAttributes

VcfDataConfig - Class in org.molgenis.data.vcf

VcfDataConfig() - Constructor for class org.molgenis.data.vcf.VcfDataConfig

VcfFileExtensions - Enum in org.molgenis.data.vcf

VcfImporterService - Class in org.molgenis.data.vcf.importer

VcfImporterService(DataService, PermissionSystemService, MetaDataService) - Constructor for class org.molgenis.data.vcf.importer.VcfImporterService

VcfRepository - Class in org.molgenis.data.vcf

Repository implementation for vcf files.

VcfRepositoryCollection - Class in org.molgenis.data.vcf

VcfRepositoryCollection(File) - Constructor for class org.molgenis.data.vcf.VcfRepositoryCollection

VcfToEntity - Class in org.molgenis.data.vcf.format

VcfToEntity(String, VcfMeta, VcfAttributes, EntityTypeFactory, AttributeFactory) - Constructor for class org.molgenis.data.vcf.format.VcfToEntity

VcfUtils - Class in org.molgenis.data.vcf.utils

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