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.

valr 0.8.4

• Update a test for compatibility with forthcoming ggplot2 3.6.0 (#431)

valr 0.8.3

• read_bigwig() now uses cpp11bigwig on CRAN. The set_strand param was removed to be
  more consistent with expected bigWig contents.

• read_gtf() was deprecated. The rtracklayer package used
  for this functionality is no longer a dependency of valr due to errors from
  CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.

• valr now depends on R >= 4.0.0.

valr 0.8.2

• Address NOTE on CRAN about Rd link targets.

• Change maintainer email address.

valr 0.8.1

• Make vdiffr dependency optional during package testing.

valr 0.8.0

• Added bed_genomecov() to compute interval coverage across a genome.

valr 0.7.0

• read_bed and related functions now automatically calculate the fields. Use of n_fields was deprecated.

valr 0.6.8

• bed_closest() now reports all x intervals, even when there are no closest y intervals (e.g. when there is no matching chromosome in y intervals). These intervals are returned populated with NA for .overlap, .dist and y interval locations.

• Reimplemented bed_closest() to use binary search rather than an interval tree search. The closest y interval can be missed with the previous search strategy in high depth interval trees.

• Fix off by one error when using max_dist argument in bed_cluster() (#401).

v0.6.7

• Removed SystemRequirements from DESCRIPTION to eliminate a NOTE on CRAN.

• bed_coverage() now reports intervals from x with no matching group in y (#395).

v0.6.6

What's Changed

• improvements for interactive use by @jayhesselberth in #393
• update intervaltree by @kriemo in #391

Full Changelog: v0.6.5...v0.6.6