Add submitter_exclusions to the XML-derived Parquet exporter. Direct
exclusions are normalized case-insensitively, combined with a selected named
profile, and applied without deleting imported source submissions.
Replace the full-release executable README with a concise quick start and an explicit comparison with upstream ClinVarbitration.
Add native x86-64 Windows extension builds using Rtools-provided libxml2,
zlib, and target-aware pkg-config; retain Linux, macOS, and webR builds.
Runtime artifact selection now matches exact DuckDB platform metadata and
includes both windows_amd64 and R-devel's windows_amd64_mingw identities.
Add rclinvarbitration_download_clinvar() for checksum-validated current or
monthly archived VCV XML downloads and optional flat-file validation inputs.
Download URL, digest, and source byte size can flow into the release catalogue.
Add clinvar_hpo_terms, clinvar_literature_links,
clinvar_semantic_documents, and disease-aware clinvar_gene_summaries for
semantic retrieval, gene panels, literature review, DuckLake publication,
and VariantStory integration.
Add pkgdown vignettes for the complete arbitration algorithm, storage/cache
lifecycle and measured full-release performance, and semantic/DuckLake/
VariantStory integration. Add a rendered docs/ERRATA.md audit of intentional
deviations and observed XML/flat/upstream differentials.
Execute the pinned upstream TSV algorithm on exact March 2026 flat inputs: all 4,125,389 keys and values match the package reproducer. Classify all 377 XML/flat key or value differences with source-row receipts, and quantify sample/method/observed-data/consequence XML structure coverage.
Add release-differential tests for disease keys, SCV replacement, withdrawn assertions, compound alleles, and mitochondrial locations, plus curated real HPO and PubMed context projections.
Add experimental webR/WebAssembly support. The package now builds its version-matched DuckDB extension as an Emscripten side module and has a browser smoke test that loads it and imports the compressed VCV fixture.
Project compact parser rows with the package-owned rclinvar_json_field()
scalar rather than DuckDB's separately downloadable JSON extension. Imports
now require no extension download, including in browser/webR runtimes.
Remove the premature local v1 policy suffix; preserve the pinned
cpg-clinvarbitration-2.2.11 identifier, source-order strong-review rule,
and separate disease- and allele-level decision views.
Add Parquet exporters for the VCV-derived allele policy and for direct, SQL-only reproduction of ClinVarbitration from versioned NCBI flat-file archives, plus a retained differential script for published Zenodo releases.
Retain imported SCV source order for deterministic strong-review decisions.
Bundle exact C_STRUCT_UNSTABLE extension artifacts for DuckDB v1.5.0
through v1.5.4, selected from the enabled connection's engine version.
Replace generic XML node/edge/statement persistence with a one-pass, ClinVar-specific entity scan and focused VCV, allele, location, gene, RCV, SCV, condition, observation, citation, attribute, and evidence-text relations. Staging now stores one JSON-backed row per selected entity and requires no release-wide EAV grouping. Release-scale tables use logical keys without memory-resident ART indexes, and each projection commits separately; the release catalogue marks completion and failed imports clean partial rows.
Add clinvar_disease_aggregates and clinvar_disease_submissions as direct
RCV- and SCV-level disease-policy inputs, with canonical disease identifiers
selected independently of the complete retained cross-reference relation.
Add the cpg-clinvarbitration-2.2.11 SQL policy,
configurable submitter-blinding profiles, and
clinvar_policy_pathogenic_alleles as the disease-specific P/LP join surface
for Rduckhts/DuckHTS.
Execute the README quick start against the bundled real VCV fixture. The separately receipted full-release benchmark remains file-backed and does not rerun during README rendering.
clinvar_xml_statements(path), a single-threaded libxml2 forward scan of
ClinVar VCV XML and XML.GZ releases.v1.5.3 on Unix-like hosts; it
fails closed for other engine versions.