Software Open Access

rnabioco/valr: valr 0.4.0

Jay Hesselberth; kriemo; sheridar; agillen; Ray; Ryan Mackie

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)

Files (1.8 MB)
Name Size
rnabioco/valr-v0.4.0.zip
md5:d226316e7e4726bdc04361e63fdfe742
1.8 MB Download

Share

Cite as