API Reference

Core Functions and Utilities

anyvar.anyvar	full-service interface to converting, validating, and registering biological sequence variation
anyvar.core.metadata	Define types and classes for metadata, i.e. additional descriptions on top of stored objects.
anyvar.core.objects	Provide types, classes, and functions for objects stored by AnyVar.

VCF Ingestion

anyvar.vcf.ingest

Support processing and manipulation of VCF objects.

Bulk Processing

Object Storage

anyvar.storage.base	Provide PostgreSQL-based storage implementation.
anyvar.storage.postgres	Provide PostgreSQL-based storage implementation.
anyvar.storage.mapper_registry	Central registry for all object mappers.
anyvar.storage.mappers	Object mappers for converting between VRS models and database entities.
anyvar.storage.orm	SQLAlchemy ORM models for AnyVar database schema.
anyvar.storage.no_db	Stateless storage implementation (no persistence).

Variant Translation

anyvar.translate.base	Provide base properties for Translator classes.
anyvar.translate.vrs_python	Normalize incoming variation descriptions with the VRS-Python library.

Mapping

anyvar.mapping.liftover

Defines functions used to lift over variants between GRCh37 & GRCh38