anyvar

Contents

  • Getting Started
    • Quick Start: Docker Compose
      • Prerequisites
      • Steps
    • Manual Setup
      • Prerequisites
      • Python Package
      • Storage Backend: PostgreSQL Service
      • Data Resource: UTA
      • Data Resource: SeqRepo
      • Verifying Installation
      • Optional: Queueing Configuration
        • Backend/Broker
        • Shared Working Directory
  • Features
    • Variant Object Types
    • Variant Translation
    • Variant Projection
    • VCF Ingestion and Annotation
    • Object Extensions
    • Variant Mappings
    • Categorical Variants
    • Stateless Mode
  • Usage
    • Using the Python API
      • Instantiating An AnyVar Instance
      • Basic Variant Object Operations
      • Variation Translation
      • Variation Liftover
      • Object Mappings
      • Object Extensions
      • VCF Ingest and Annotation
    • Using the REST API
      • Swagger UI Docs
      • Basic Variant Operations
      • Searching Variants
      • Bulk Variant Registration
        • Asynchronous Bulk Registration
      • Working With Mappings
      • Working With Extensions
      • VCF Annotation and Ingestion
      • Categorical Variant Registration and Retrieval
      • Get Service Info
    • Running REST Service
      • Spinning Up the REST Server
      • Storing Environment Variables
      • Stateless Annotation and Translation
  • Configuration
    • Storage
      • Storage Connection
      • Rename Tables
    • Asynchronous Processing
      • Required: Work Directory Path (VCF)
      • Broker/Backend Connection
      • Celery Task Settings
      • Misc. VCF Processing
      • Variation Registration Settings
    • Authentication
      • Authentication Modes
      • Authentication Behavior
      • Configuration Parameters
        • Literal Token Authentication
        • JWT Token Authentication
      • Example Configuration
        • Literal Token Authentication
        • JWT Token Authentication with Azure AD
        • Combined Authentication
      • Using Bearer Tokens
      • Security Considerations
    • Logging
      • Default Behavior
      • Customizing Logging Configuration
      • Applying Logging Configuration
      • Example YAML Configuration
    • Service-Info
      • Example service-info YAML file
    • Example .env file
    • Docker Compose
      • Overview
      • SeqRepo Options
        • Using the bundled SeqRepo container (default)
        • Using a host SeqRepo directory directly
        • Copying a host SeqRepo into a Docker volume
      • UTA Service Configuration
      • AnyVar Database Configuration
      • Running the stack
  • API Reference
    • Core Functions and Utilities
      • anyvar.anyvar
        • AnyVar
        • InvalidCategoricalVariantError
        • ObjectNotFoundError
        • create_projector()
        • create_storage()
        • create_translator()
        • has_queueing_enabled()
        • has_variations_queueing_enabled()
      • anyvar.core.metadata
        • Extension
        • ExtensionName
        • VariationMapping
        • VariationMappingType
      • anyvar.core.objects
        • SupportedVrsObject
        • SupportedVrsVariation
        • recursive_identify()
      • anyvar.core.categorical_variants
        • CanonicalAllele
        • ProteinSequenceConsequence
        • get_molecule_type()
        • is_expected_molecule_type()
    • VCF Ingestion
      • anyvar.vcf.ingest
        • RequiredAnnotationsError
        • VcfRegistrar
        • VrsObjectRegistrationBatcher
        • register_existing_annotations()
    • Bulk Processing
    • Object Storage
      • anyvar.storage.base
        • AlleleSearchPage
        • DataIntegrityError
        • IncompleteVrsObjectError
        • InvalidSearchParamsError
        • MissingVariationReferenceError
        • Storage
        • StorageError
      • anyvar.storage.postgres
        • PostgresObjectStore
      • anyvar.storage.duckdb
        • DuckDbObjectStore
      • anyvar.storage.mapper_registry
        • MapperRegistry
      • anyvar.storage.mappers
        • AlleleMapper
        • BaseMapper
        • CanonicalAlleleMapper
        • ExtensionMapper
        • ProteinSequenceConsequenceMapper
        • SequenceLocationMapper
        • SequenceReferenceMapper
        • VariationMappingMapper
      • anyvar.storage.orm
        • Allele
        • Base
        • CanonicalAllele
        • Extension
        • Location
        • ProteinSequenceConsequence
        • SequenceReference
        • VariationMapping
        • VrsObject
        • create_tables()
        • session_factory()
      • anyvar.storage.no_db
        • NoObjectStore
    • Variant Translation
      • anyvar.translate.base
        • TranslationError
        • Translator
        • TranslatorConnectionError
        • TranslatorSetupError
      • anyvar.translate.vrs_python
        • VrsPythonTranslator
        • WindowedSeqRepoDataProxy
      • anyvar.translate.register
        • add_projection_mappings()
        • register_variations()
        • translate_variation()
    • Mapping
      • anyvar.mapping.liftover
        • AccessionConversionError
        • AmbiguousCoordinateConversionError
        • CoordinateConversionFailureError
        • LiftoverError
        • ReferenceAssembly
        • RoundtripError
        • UnsupportedReferenceAssemblyError
        • UnsupportedVariantLocationTypeError
        • convert_position()
        • liftover_and_register_variant()
        • liftover_variant()
      • anyvar.mapping.projection_models
        • ProjectedVariation
        • ProjectionError
        • ProjectionFailure
        • ProjectionNotApplicable
        • ProjectionResults
      • anyvar.mapping.protocols
        • VariantProjectorProtocol
        • project_and_register_variations()
  • Getting Help
  • Changelog
    • 1.1.0-dev0
    • 1.0.0
    • 1.0.0-rc3
    • 1.0.0-rc2
    • 1.0.0-rc1
    • 0.9.1
    • 0.9.0
  • Contributing
    • Installing For Development
    • Testing
    • Documentation
  • License
anyvar
  • Search

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