as.tbl_interval() to call as_tibble() only on non-tibble input, which prevents groups from being stripped from tibble() input (#338).Added new function, bed_partition(), which is similar to bed_merge() but collapses intervals to elemental intervals rather than the maximal overlapping region. bed_partition() also can compute summaries of data from overlapping intervals. See examples in bed_partition() and timings in vignette('benchmarks') @kriemo.
Several explicit comparisons to the Bioconductor GenomicRanges library are included for users considering using valr. See examples in as.tbl_interval() and timings in vignette('benchmarks').
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).
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)
A manuscript describing valr has been published in F1000Research.
New S3 generic as.tbl_interval() converts GenomicRanges::GRanges objects to tbl_interval.
New create_tss() for creating transcription start sites.
Improve documentation of interval statistics with more complex examples.
bed_sort() has been de-deprecated to reduce arrange calls in library code.bed_merge() now reports start/end columns if spec is provided (#288)New create_introns(), create_utrs5() and create_utrs3() functions for generating features from BED12 files.
Speed-ups in bed_makewindows() (~50x), 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).
new tbl_interval() and tbl_genome() that wrap tibbles and enforce strict column naming. trbl_interval() and trbl_genome() are constructors that take tibble::tribble() formatting and is.tbl_interval() and is.tbl_genome() are used to check for valid classes.
bed_random() are sorted by chrom and start by default.bed_jaccard() and use numeric values for calculation (fixes #204).bed_sort() in favor of using dplyr::arrange() explicitly (fixes #134).add src/init.c that calls R_registerRoutines and R_useDynamicSymbols to address NOTE in r-devel
Deprecate dist parameter in bed_closest() in favor of using user supplied functions (#182 @kriemo)
Make .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