valr 0.9.0

Breaking changes

• Added min_overlap parameter to bed_intersect(), bed_subtract(), bed_coverage(), and bed_map(). The default min_overlap = 1L aligns with bedtools behavior where book-ended (adjacent) intervals are not considered overlapping. Use min_overlap = 0L to preserve the previous valr behavior where book-ended intervals were treated as overlapping. Currently, calling these functions without an explicit min_overlap value will emit a deprecation warning and use the legacy behavior (min_overlap = 0L). In a future release, the default will change to min_overlap = 1L, so users should update their code to explicitly specify the desired behavior.

Major changes

• Migrated C++ backend from Rcpp to cpp11. This modernizes the codebase and removes the Rcpp dependency. All interval operations maintain identical behavior.

Minor changes

• Eliminated all global variable dependencies by replacing bare column names with explicit .data[["column"]] syntax in data manipulation operations and all_of() in column selection operations.

• Fixed bed_makewindows() step size calculation when step_size parameter is used. Previously, overlapping windows stepped by win_size - step_size instead of the specified step_size (#438).

• Select methods (tibble, tribble) are now re-exported from the tibble package.

• read_bigbed() is now re-exported from the cpp11bigwig package.