NEWS

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DuckDBGRanges 0.99.1

Documentation

• Added \value sections (roxygen @return) to the DuckDBGRanges and DuckDBGRangesList class and utility man pages, documenting the values returned by the constructors, accessors, replacement, coercion, and range-operation methods. Resolves the R CMD BiocCheck "missing \value" WARNING.

DuckDBGRanges 0.9.8

Testing and diagnostics

• Added a query-plan regression guard for interval overlaps (no change to overlap results or their current speed). A new internal .explainQuery() returns DuckDB's plan for a lazy query, and a test uses it to assert the overlap join stays an IEJoin / range join rather than degrading to a NESTED_LOOP_JOIN over the full cross product (which OOMs on skewed inputs). Interval overlap is a range join, not an ASOF (nearest-match) join. The overlap join was factored into an internal .overlap_join_tbl() helper so its plan can be inspected without collecting.

DuckDBGRanges 0.9.7

Changes

• Relicensed under the MIT License.

DuckDBGRanges 0.9.6

Bug fixes

• precede()/follow() with select = "all" now return only the subject(s) at the nearest distance (the ties), matching base GenomicRanges — previously they returned every directional subject. The select = "first"/"last" paths were already correct; the "all" branch was missing the min-distance filter.
• distance() now returns NA for a paired range on a different seqname or (unless ignore.strand = TRUE) an incompatible strand (+ vs -; * matches any strand), matching base GenomicRanges::distance. Previously it ignored seqnames and strand and returned a bare coordinate gap. Added an ignore.strand argument.

DuckDBGRanges 0.9.5

Bug fixes

• narrow() now treats a negative start as a position counting back from the range end (-1 is the last base), matching base IRanges::narrow (solveUserSEW) and the existing negative-end behaviour. Previously a negative start was applied as start + (start - 1), walking left of the range start and producing an invalid interval. The start/end/width expressions are rebuilt so every sign-and-width combination is correct; because the datacols expressions flatten to SQL without parentheses, each is kept as a column +/- scalar (never a subtraction of a compound). Oracle-tested against base narrow across positive/negative start/end and their width combinations.
• nearest(x) and distanceToNearest(x) (no subject) now exclude self-hits, matching base GenomicRanges' drop.self = TRUE for the missing-subject form: a range is never its own nearest neighbour, so its next-nearest is returned instead of itself (distance 0). Previously both delegated to the two-argument form against x itself, so every range matched itself. The explicit nearest(x, x) / distanceToNearest(x, x) forms still keep self-hits, as in base. (precede/follow were already correct — their strict inequalities never admit a self-match.) Added a self-query test comparing to the base oracle.
• nearest/precede/follow/distanceToNearest now treat strand "*" as compatible with any strand, matching base GenomicRanges: "+" pairs with {+,*}, "-" with {-,*}, and "*" with all. The neighbour join used a strict equi-join on strand, which silently dropped every "*" pair (a "*" query against "+"/"-" subjects returned NA). The join is now on seqnames only, followed by a strand-compatibility filter.
• precede() and follow() are now strand-directional. Base defines them in the transcription direction — for a "-" strand query the roles of upstream and downstream are reversed, and for a "*" query the direction is chosen per subject strand. The previous implementation used a fixed genomic-coordinate direction regardless of strand, so results were inverted on the "-" strand. The convention is now selected per row (subj_start > end vs subj_end < start) via use_minus = strand == "-" | (strand == "*" & subj_strand == "-"), ranking by the transcription-direction gap; ignore.strand = TRUE collapses to the "+" convention as before. follow() keeps its base select = "last" (largest index) tie-break, precede() its select = "first" (smallest index). Added oracle tests against base GenomicRanges across +/-/* queries with mixed-strand subjects, plus tie-break tests.

DuckDBGRanges 0.9.4

Bug fixes

• resize(x, width, fix = "center") now matches base IRanges::resize(): new_start = start + (width(x) - width) %/% 2, anchored at the (strand-independent) center with an exact integer width. The previous implementation used the midpoint (start + end) / 2 with true division --- yielding fractional coordinates for even-width ranges --- and center + width %/% 2 - 1, which returned width - 1 for odd target widths. Added fix = "center" cases to the resize tests.

DuckDBGRanges 0.9.3

Documentation

• Restructured the vignettes into a user-first set, replacing the single internals-heavy Architecture of the DuckDBGRanges Package:
  • Introduction to DuckDBGRanges --- motivation, construction, and the common operations (accessors, subsetting, range operations, the filter-then-materialize workflow, DuckDBGRangesList).
  • Benchmarking DuckDBGRanges --- a best-effort comparison against in-memory GRanges on scATAC-seq (1M peaks) and variant (10M variants) scenarios, rendered from precomputed results so the vignette builds quickly.
  • Design and extension of DuckDBGRanges --- the five coordinate columns, class structure, SQL translation, and the LIST[] representation of grouped ranges, for developers.
• Added inst/scripts/ with the offline benchmark generator (run_vignette_benchmarks.R) and the vignette table helpers (make_timings_table.R), following the HDF5Array performance-vignette precompute pattern.
• Rewrote the README.