NEWS

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XCNV 0.0.0.9000

• Bundled the published 41-node X-CNV classifier as a validated runtime-neutral R data object, and made it the default when an annotation resource directory does not supply an override. Runtime prediction remains independent of XGBoost.
• Bundled a compact real ClinVar 72461/SOX2 example with its case-local X-CNV annotations and objective GENCODE/ClinGen content evidence.
• Corrected the published-resource readers: LJB26 START == END records are one-base points rather than empty BED intervals, LJB scores are selected by their explicit site index, and the headerless merged-sample file retains its first observation.
• Added an installable R package API for reading CNV tables, validating resource bundles, computing X-CNV annotations, predicting MVP scores, and writing the legacy table format.
• Added a small deterministic fixture and tinytest coverage, including an independent R overlap oracle for the production DuckDB inequality join.
• Removed bedtools and XGBoost from the installed runtime. A deterministic staging script converts a separately obtained XGBoost model to a validated, tabular xcnv-tree-v1 artifact; the package evaluates that artifact in R.
• Added an independently authored ACMG/ClinGen 2019 constitutional-CNV scoring contract with provenance-required evidence rows, published score ranges, criterion-group caps, and five-tier classification. A DuckDB-backed content provider derives only sections 1, 2A, and 3 from explicit gene and ClinGen dosage relations; case, phenotype, inheritance, partial-gene, and population evidence remain curator/provider inputs.
• Recorded the pinned upstream compatibility scope and current resource limitations.