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Changelog

Source: NEWS.md

RClinVarbitration 0.1.1

  • 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  • Add release-differential tests for disease keys, SCV replacement, withdrawn assertions, compound alleles, and mitochondrial locations, plus curated real HPO and PubMed context projections.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.

RClinVarbitration 0.1.0

  • First public release.
  • Added a package-owned DuckDB C extension with clinvar_xml_statements(path), a single-threaded libxml2 forward scan of ClinVar VCV XML and XML.GZ releases.
  • Added semantic SQL materialization for ordered XML nodes, edges, literals, and discovery text, with a real NCBI VCV XML.GZ fixture.
  • The first artifact supports exactly DuckDB v1.5.3 on Unix-like hosts; it fails closed for other engine versions.