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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
    • VCF Ingestion and Annotation
    • Object Annotations
    • Variant Mappings
    • Stateless Mode
  • Usage
    • Using the Python API
      • Instantiating An AnyVar Instance
      • Basic Variant Object Operations
      • Variation Translation
      • Variation Liftover
      • Object Mappings
      • Object Annotations
      • VCF Ingest and Annotation
    • Using the REST API
      • Swagger UI Docs
      • Basic Variant Operations
      • Searching Variants
      • Working With Mappings
      • Working With Annotations
      • VCF Annotation and Ingestion
      • Get Service Info
    • Running REST Service
      • Spinning Up the REST Server
      • Storing Environment Variables
      • Stateless Annotation and Translation
  • Configuration
    • Storage
      • Storage Connection
      • Rename Tables
    • Snowflake Storage
      • Setting up Snowflake
      • Data Management Configuration Options
        • Dynamic Tables
        • Join-Based Merge
        • Default Configuration
    • Asynchronous Processing
      • Required: Work Directory Path
      • Broker/Backend Connection
      • Celery Task Settings
      • Misc. VCF Processing
    • 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
        • ObjectNotFoundError
        • create_storage()
        • create_translator()
        • has_queueing_enabled()
      • anyvar.core.metadata
        • Annotation
        • AnnotationType
        • VariationMapping
        • VariationMappingType
      • anyvar.core.objects
        • VrsObject
        • VrsVariation
        • recursive_identify()
    • VCF Ingestion
      • anyvar.vcf.ingest
        • RequiredAnnotationsError
        • VcfRegistrar
        • VrsObjectRegistrationBatcher
        • register_existing_annotations()
    • Bulk Processing
    • Object Storage
      • anyvar.storage.base
        • DataIntegrityError
        • IncompleteVrsObjectError
        • InvalidSearchParamsError
        • MissingVariationReferenceError
        • Storage
        • StorageError
      • anyvar.storage.postgres
        • PostgresObjectStore
      • anyvar.storage.mapper_registry
        • MapperRegistry
      • anyvar.storage.mappers
        • AlleleMapper
        • AnnotationMapper
        • BaseMapper
        • SequenceLocationMapper
        • SequenceReferenceMapper
        • VariationMappingMapper
      • anyvar.storage.orm
        • Allele
        • Annotation
        • Base
        • Location
        • SequenceReference
        • SnowflakeVARIANT
        • 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
    • Mapping
      • anyvar.mapping.liftover
        • AccessionConversionError
        • AmbiguousCoordinateConversionError
        • CoordinateConversionFailureError
        • LiftoverError
        • ReferenceAssembly
        • UnsupportedReferenceAssemblyError
        • UnsupportedVariantLocationTypeError
        • add_liftover_mapping()
        • convert_position()
        • get_liftover_variant()
  • Getting Help
  • Changelog
    • 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
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  • Search

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