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)
Fixed off by one error in reported distances from
bed_closest(). Distances reported now are the same as
bedtools closest behavior (#311).
trbl_intervals named other than
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
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)
A manuscript describing valr has been published in F1000Research.
New S3 generic
GenomicRanges::GRanges objects to
create_tss() for creating transcription start sites.
Improve documentation of interval statistics with more complex examples.
bed_sort()has been de-deprecated to reduce
arrangecalls in library code.
bed_merge()now reports start/end columns if spec is provided (#288)
create_utrs3() functions for generating features from BED12 files.
bed_merge() (~4x), and
bed_flank() (~4x) (thanks to @kriemo and @sheridar). Thanks to the sponsors of the Biofrontiers Hackathon for the caffeine underlying these improvements.
bed_random()are now sorted properly.
Package dplyr v0.5.0 headers with valr to remove dplyr LinkingTo dependency.
bed_intersect() now accepts multiple tbls for intersection (#220 @kriemo).
tbl_genome() that wrap tibbles and enforce strict column naming.
trbl_genome() are constructors that take
tibble::tribble() formatting and
is.tbl_genome() are used to check for valid classes.
bed_random()are sorted by
bed_jaccard()and use numeric values for calculation (fixes #204).
bed_sort()in favor of using
dplyr::arrange()explicitly (fixes #134).
src/init.c that calls
R_useDynamicSymbols to address NOTE in r-devel
dist parameter in
bed_closest() in favor of using user supplied functions (#182 @kriemo)
.id values sequential across chroms in
bed_cluster() output (#171)
Transfer repository to http://github.com/rnabioco/valr, update links and docs.
Move shiny app to new repo (http://github.com/rnabioco/valrdata).
Add Kent Riemondy to LICENSE file.
bed_merge()now merges contained intervals (#177)
test / vignette guards for Suggested RMySQL
fixed memory leak in absdist.cpp
fixed vignette entry names