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valr 0.4.2.9000

valr 0.4.2

Bug fixes

  • Changed the behavior of as.tbl_interval() to call as_tibble() only on non-tibble input, which prevents groups from being stripped from tibble() input (#338).

valr 0.4.1

  • 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').

valr 0.4.0

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

Enhancements

  • 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.

Minor changes

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

Bug fixes

  • bed_merge() now reports start/end columns if spec is provided (#288)

valr 0.3.0

Enhancements

  • 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.

Bug fixes

  • intervals from bed_random() are now sorted properly.

valr 0.2.0

Major changes

  • 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.

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

Major changes

  • Deprecate bed_sort() in favor of using dplyr::arrange() explicitly (fixes #134).

Minor changes

  • 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.

Bug fixes

  • bed_merge() now merges contained intervals (#177)

valr 0.1.1

Minor changes

  • test / vignette guards for Suggested RMySQL

  • fixed memory leak in absdist.cpp

  • fixed vignette entry names

valr 0.1.0

Major changes

  • initial release on CRAN