Compute the coding, genome-wide, regulatory, haploinsufficiency, and
population-frequency features used by X-CNV. Overlap is computed in-process
using BED half-open interval arithmetic; the reciprocal 0.5 thresholds used
by the upstream frequency step are retained. CNV lengths use the upstream
inclusive end - start + 1 convention.
Usage
annotate_cnv(x, resources, overlap_backend = c("duckdb", "reference"))
Arguments
- x
A path, data frame, or matrix containing CNV records.
- resources
An xcnv_resources object or an explicit resource directory.
- overlap_backend
"duckdb" for the production inequality-join path,
or "reference" for the small brute-force correctness oracle.
Value
A data frame in legacy feature order, with the input columns first,
the model and auxiliary annotation columns next, and Type.1 and
Length at the end.