Guides machine-readable function catalogs for DuckDB extensions, including a `functions.yaml` source-of-truth pattern that can drive docs, wrappers, aliases, examples, and consistency checks. Use when an extension exposes many SQL functions or multiple wrapper surfaces.
Guides development in the DuckHTS repo, including DuckDB extension work, Rduckhts package integration, vendored htslib workflows, SQL and tinytest coverage, wasm/webR constraints, and exact-compatible rewrites of upstream genomics tools. Use when working in github.com/RGenomicsETL/duckhts.
Guides creation, maintenance, checking, testing, documenting, and releasing R packages using project-native workflows such as Makefiles, tinytest, roxygen2, base R, and optional tools like usethis, pkgdown, air, or jarl. Use when working on any R package or CRAN-style package workflow.
Guides cache, index, and annotation-store design for bioinformatics rewrites, including when to use mainstream interoperable formats versus specialized high-performance encodings. Use when startup cost, repeated lookup performance, interval access, or annotation storage strategy are central design concerns.
Guides library-first bioinformatics rewrites that expose mature native code through bindings, extensions, FFI, or embedded runtimes across R, Python, SQL, and wasm. Use when building reusable interfaces around existing C/C++ libraries instead of standalone-only rewrites.
Guides responsible AI-assisted rewriting and porting of bioinformatics tools, combining rewrites.bio principles with practical validation, attribution, compatibility, and maintenance discipline. Use when planning or implementing a rewrite, reimplementation, or high-performance port of an existing bioinformatics tool.
Guides design of bioinformatics kernels and rewrites that compute multiple validated outputs or statistics in one pass over the data, reducing repeated I/O and decompression while preserving explicit semantics. Use when designing fused readers, counters, coverage engines, or summary pipelines.
Guides DuckDB C extension API selection, deprecation handling, compatibility shims, and release policy. Use when balancing stable versus unstable APIs, managing breaking changes, or documenting deprecation strategy for SQL and wrapper surfaces.