Components and maturity¶
Altar distinguishes stable interfaces from reference implementations and experimental features.
- Stable interface Compatibility-controlled façade used by external packages.
- Reference Maintained implementation suitable within its documented scale and constraints.
- Provisional interface Exported from a stable façade, but not yet covered by its compatibility commitment because it lacks a public adapter, a consumer, or conformance coverage. See provisional names.
- Experimental Available for evaluation, but not covered by the stable façade policy.
Scientific integrations¶
See current scope for genome-build and variant-type limits that apply across integrations.
| Integration | Form | Genome scope | Status | Installation |
|---|---|---|---|---|
| ChromBPNet | executable model binding + TensorFlow runtime | configured model/genome artifacts | Reference | altar-chrombpnet; separate runtime image |
| Cherimoya | executable model binding + PyTorch runtime | configured model/genome artifacts | Reference | altar-cherimoya; separate runtime image |
| Enformer | executable model binding + TensorFlow runtime | hg38; configured track selection | Reference | altar-enformer; separate runtime image |
| Borzoi | executable model binding + TensorFlow runtime | hg38; selected GTEx tracks | Reference | altar-borzoi; separate runtime image |
| LegNet | executable model binding + PyTorch runtime | hg38; configured checkpoint cell type | Reference | altar-legnet; separate runtime image |
| Sei | executable model binding + PyTorch runtime | hg19 or hg38 | Experimental; not yet validated against the official weights | altar-sei; separate runtime image |
| AlphaGenome | hosted API model binding | configured organism, ontology terms, and scorers | Experimental scientific policy; maintained adapter | altar-alphagenome |
| GPN-Star | precomputed SNV annotation source | release-dependent; includes hg38 and non-human assemblies | Reference | altar-gpnstar + prepared Parquet assets |
| SpliceAI | precomputed annotation source | hg38 dataset supplied by user | Reference | altar-spliceai + licensed upstream data |
| AlphaMissense | precomputed annotation source | hg38 dataset supplied by user | Reference | altar-alphamissense + upstream data |
| gnomAD | population allele-frequency annotation source | gnomAD v4 on hg38; genomes, exomes, or joint | Reference | altar-gnomad + upstream sites VCFs |
| ClinVar | germline-classification annotation source | ClinVar releases from 20240127 on, GRCh38 (hg38) or GRCh37 (hg19, without MT) | Reference | altar-clinvar + upstream VCF |
| Open Targets E2G | variant-to-gene relation source | configured Open Targets release/build | Reference | altar-opentargets-e2g + generic link store |
| ENCODE-rE2G + scE2G atlases | variant-to-gene relation source | GRCh38; ENCODE DCC accessions and scE2G v1.3 multiome schema | Reference | altar-e2g-atlas + generic link store |
Infrastructure implementations¶
| Capability | Implementations | Status |
|---|---|---|
| task execution | local Docker, Modal, Kubernetes | Reference |
| score storage | SQLite, BigQuery | Reference |
| annotation storage | SQLite, BigQuery | Reference |
| variant–gene link storage | in-memory, SQLite | Reference |
| object storage | local filesystem | Reference |
job queue (JobQueue, provisional interface) |
none; InMemoryJobQueue test double only |
Provisional |
authentication (AuthProvider, provisional interface) |
development token provider | Provisional; development only |
| investigation agent | LangGraph graph, reference SQLite host | Experimental |
Stable public modules¶
External extensions should import from altar.models, altar.execution, altar.results, altar.sources,
altar.predicates, altar.registry, altar.access, altar.scoring, altar.testing, and altar.variants. See the
compatibility policy.
Variant and file identity live in altar-identity, a separate, dependency-free distribution for Python 3.9
and later that Altar installs automatically. It defines VariantKey, the chromosome and variant-ID rules,
SHA-256 file digests and verification records, and the variant file Altar stages for a model container.
altar.models, altar.sources, altar.variants, and altar.execution re-export its variant-key names and
verification-record helpers, and bindings import them from there. Model runtimes import altar_identity directly. See
the identity package.
The job-queue and authentication contracts are provisional: every name in altar.access, JobQueue and
get_job_queue_registry in altar.execution, and their conformance suites in altar.testing. They remain
importable from these modules but may change in a minor release.