valr 0.4.0.9000 Unreleased

valr 0.4.0 2018-01-25

Minor changes

  • All relevant tests from bedtool2 were ported into valr. Bugs identified in corner cases by new tests were fixed (#328 @raysinesis)

  • bed_jaccard() now works with grouped inputs (#216)

  • Update dplyr header files to v0.7

  • bed_intersect() and internal intersect_impl were refactored to enable return of non-intersecting intervals.

  • The genome argument to bed_makewindows() was deprecated and will produce a warning if used. Also error handling was added to check and warn if there are intervals smaller than the requested window size in makewindows_impl() (#312 @kriemo)

Bug fixes

  • Fixed off by one error in reported distances from bed_closest(). Distances reported now are the same as bedtools closest behavior (#311).

  • bed_glyph() accepts trbl_intervals named other than x and y (#318).

  • bed_makewindows() now returns the number of windows specified by num_win when the input intervals are not evenly divisble into num_win, consistent with bedtools behavior.

  • The output of findOverlaps() is now sorted in subtract_impl() to prevent reporting intervals that should have been dropped when calling bed_subtract() (#316 @kriemo)

valr 0.3.1 2017-07-22

Enhancements

Minor changes

  • bed_sort() has been de-deprecated to reduce arrange calls in library code.

Bug fixes

valr 0.3.0 2017-06-15

Enhancements

Bug fixes

valr 0.2.0 2017-05-05

Major changes

Minor changes

  • intervals returned from bed_random() are sorted by chrom and start by default.

Bug fixes

  • Merge intervals in bed_jaccard() and use numeric values for calculation (fixes #204).

valr 0.1.2 2017-03-16

Major changes

Minor changes

Bug fixes

valr 0.1.1 2016-12-01

Minor changes

  • test / vignette guards for Suggested RMySQL

  • fixed memory leak in absdist.cpp

  • fixed vignette entry names

valr 0.1.0 2016-11-21

Major changes

  • initial release on CRAN