Boundary | Backends | R surface | Validation

Scope and authority | Inputs retained for arbitration | Step 1: classification bins | Step 2: exclusions | Step 3: SCV version deduplication | Step 4: 2016 evidence window | Step 5: decisive strong review | Step 6: 60/20 arbitration | Step 7: star assignment | Disease identity | Output and audit columns | Complete-release differential validation

Motivation beyond variant annotation | Discovery-oriented views | Using ducksemantics | Publishing releases to DuckLake | VariantStory boundary | Talos 11.1 compatibility target

What is cached? | Download cache | Exact DuckDB extension artifacts | Persistent relational release store | Import lifecycle | What remains virtual? | Measured complete-release conversions

1. HTTP Client | ncurl: Basic Requests | ncurl_aio: Async Requests | Promises Integration | ncurl_session: Persistent Connections | 2. WebSocket Client | 3. Unified HTTP/WebSocket Server | Handler Types | HTTP Request Handlers | Static Content Handlers | WebSocket Handlers | HTTP Streaming Handlers | Server-Sent Events | 4. Secure Connections (TLS) | Public Internet HTTPS | Self-Signed Certificates | 5. Client Example: Shiny ExtendedTask | 6. Server Example: Quarto Site with Dynamic API | 7. Server Deployment with _server.yml

Task states | Leases fence stale workers | Failures and the retry budget | Supervise work longer than a lease | Checkpoints keep R values | Query state with SQL | Abandoned tasks and native maintenance | Error classification | Limits

Run a task | Resume after a failure | Sleep durably | Watch tasks | Samples, then a cohort | Worker lifetime

Field names | Known driver and engine issues | VARIANT conversion under garbage collection | Nested NULLs | Indexed VARIANT field extraction | How values are read

Base R | qs2 | Sakura: rebuilding reference objects | Your responsibilities

Build a tiny alignment batch | The downstream C consumer | Compile and call it with Rtinycc | Lossless query-group stream

Why Rducks ships exact-version extensions | Runtime selection | Unsupported versions | Maintainer workflow

Setup | Why a bridge is needed | Register selected R helpers for duckplyr | Why scalar mode is the default | Execution plans: in-process and worker-process | Cleanup

Supported transports | Select the plan before registration | Worker-process (ipc) plan | Inspect workers | What rducks_release() does

Source and installed layout | Package and extension split | Runtime scopes | R-thread discipline | Scalar UDF registration and execution | Aggregates | Table functions | Query streams | IPC provider lifecycle | Ownership and copying model

Contract | Select an installed genetic map | Chunk and split the reference | Phase and ligate | SIMD selection

Tables and coordinates | Opaque metadata | Source-population ancestry | Round trips

Enable Rducks | Register a scalar UDF | Register an aggregate | Register a table function | Stream query results back to R | Release connection-local state

1. Request Reply Protocol | 2. Publisher Subscriber Protocol | 3. Surveyor Respondent Protocol | 4. Device (Broker / Proxy)

Pin file | Patch queue | Developer checkout | Vendored source

Function kind, scalar-UDF mode, and execution plan | Declared descriptors | NULL handling | Error handling and side effects | Runtime reference tables

Async-first surface | Usage from another R package | Minimal usage pattern | Prefix-scoped byte stores | Why this exists

A small explicit format layer | Add an explicit cache

Write an object and an index | Read selected records by range | Async and byte handles

Root-relative paths | Range-heavy readers | Zarr-like byte stores | Control knobs belong in handles | Error values are first-class

Submit and wait | Poll or race | Coordinating several handles with condition variables

S3-compatible examples | Google Drive | Azure Blob / GCS helpers

Aio pattern with the same API

Raw and text modes | Serializers for R objects | Native codecs

Dataflow | Async and thread safety | Serialization and codecs pipeline | Layer controls | API boundaries by function family

Core Concepts | Key Takeaways | 1. Sockets and Connections | Create Sockets | Protocols | Transports | 2. Send and Receive | Synchronous | Receive Modes | 3. Async I/O | Basic Async | Non-blocking Patterns | 4. Condition Variables | Basics | Pipe Notifications | Async with CV | 5. Request/Reply (RPC) | Server | Client | 6. Pub/Sub | 7. Surveyor/Respondent | 8. TLS Secure Connections | Self-signed Certificates | CA Certificates | 9. Options and Statistics | Get/Set Options | Common Options | Custom Serialization | Statistics | 10. Contexts | 11. Cross-language Exchange | R to Python (NumPy) | 12. Error Handling | 13. Utilities

1. TLS Secure Connections | 2. Options | 3. Custom Serialization | 4. Statistics

1. Cross-language Exchange | 2. Async and Concurrency | 3. Synchronisation Primitives