Changelog

Spencer Nystrom has made several significant contributions to the join_nearest family of functions:
1. join_nearest_(x, y, ..., distance = TRUE) family of functions now takes a new argument, distance, which allows the user to add a column for the distance of the nearest range y to that in x.
2. add_nearest_distance_(x, y, ...) family of functions, which will add a new metadata column to the x ranges object which contains the distance to its nearest neighbor in y. If there are no nearest neighbors, the new column will be given a missing value.

refactoring of select internals, improved speed when casting a GRanges -> DataFrame

update handling of list columns, expand_ranges() no longer takes cartesian product if lists are parallel. summarize() properly handles list column output without blowing out number of columns.

fixed issue #62 for Ranges construction, the as_granges() and as_iranges() functions now handle List columns correctly
added in helper functions for dealing with names in Ranges. See ?ranges-names for details.

added slice() for Ranges, and GroupedRanges
internals of grouping have been overhauled, but there shouldn’t be any user facing changes. It is now much faster to generate groupings.
group information can be interrogated with dplyr::group_keys()
a GRangesList can be obtained automatically from a GroupedGenomicRanges with dplyr::group_split()
group indices can be generated with dplyr::group_indices()

shift_downstream() and shift_upstream() now properly handle vector amounts of shift. Fixes issue #73

Left outer join overlap operations now work if either x or y have no metadata columns see #70
Left outer join overlap operations will also correctly behave in situations when there are no non-overlapping ranges.
Left outer join overlaps no longer modify seqinfo (see here)[https://support.bioconductor.org/p/125623/]
patch left outer join when x or y are IRanges, flesh out overlaps documentation.

plyranges release and devel have removed unnest() and replaced it with expand_ranges() due to changes in the tidyr API. Please replace all uses of this function with expand_ranges()

enable right generics to be called upon invoking plyranges functions without loading plyranges

refactored set_width out so it’s called internally by mutate
along with set_width there are other internal set_ methods
add _within_directed variants for overlaps methods
modified overscope_ranges to be an S3 method, should enable more refactoring in the future

package passed review and is now on Bioconductor devel branch!
I’ve been pretty slack with updating the NEWS file but will be more diligent in the future.

plyranges 1.9.3