NEWS.md

In valr: Genome Interval Arithmetic

valr 0.7.0

• read_bed and related functions now automatically calculate the fields. Use of n_fields was deprecated.

valr 0.6.8

• bed_closest() now reports all x intervals, even when there are no closest y intervals (e.g. when there is no matching chromosome in y intervals). These intervals are returned populated with NA for .overlap, .dist and y interval locations.

• Reimplemented bed_closest() to use binary search rather than an interval tree search. The closest y interval can be missed with the previous search strategy in high depth interval trees.

• Fix off by one error when using max_dist argument in bed_cluster() (#401).

valr 0.6.7

• Removed SystemRequirements from DESCRIPTION to eliminate a NOTE on CRAN.

• bed_coverage() now reports intervals from x with no matching group in y (#395).

valr 0.6.6

• Updated intervalTree header to commit f0c4046

• valr now uses cli for more consistent errors and messages during interactive use.

• deprecated genome argument to bed_makewindows() was removed.

valr 0.6.5

• Handle max_dist for first intervals in bed_cluster() (#388)

valr 0.6.4

• Fixed intron score numbering error in create_introns (#377 @sheridar)

• Fixed bug in handling of list inputs for bed_intersect()(#380 @sheridar)

• Added read_bigwig and read_gtf functions to import data into valr compatible tibbles (#379)

• Kent Riemondy is now maintainer.

valr 0.6.3

• Update to prepare for readr 2.0.0

valr 0.6.2

Minor changes

• RMariaDB has replaced the deprecated RMySQL package as the database backend.

• valr now imports Rcpp, which should have always been the case, but was masked by its Import by readr, which recently dropped use of Rcpp.

valr 0.6.1

Bug Fixes

• Fixed rchk unprotect error (#365)

valr 0.6.0

Major changes

• trbl_interval() and trbl_genome() custom tibble subclasses have been deemed unnecessary and have been removed from the package.

• coercing GRanges to a valr compatible data.frame now uses the gr_to_bed() function rather than as.trbl_interal() methods.

Minor changes

• dplyr version < 0.8.0 is no longer supported due to unnecessary code bloat and challenges with handling multiple grouping structures (#359).

• The sort_by argument of bed_random() has been changed to sorted, and will now by default use bed_sort() to sort the output, rather than rely on naming the sorting columns. Sorting can be suppressed by using sorted = FALSE.

• bed_sort() now uses base R sorting with the radix method for increased speed. (#353)

• tbls processed by bed_merge()or bed_sort() no longer store either merged or sorted as attributes, due to these attributes being rarely checked in the codebase and potential sources of unexpected behavior.

Bug fixes

• Fixed bed_closest() to prevent erroneous intervals being reported when adjacent closest intervals are present in the y table. (#348)

• Factor columns that are not used for grouping are returned as factors rather than inappropriately being coerced to integer vectors (#360)

valr 0.5.0

Major changes

• Internal Rcpp functions have been reorganized to remove all dependencies on dplyr C++ functions.

Minor changes

• Due to internal refactoring of Rcpp functions, only data.frames containing Numeric, Logical, Integer, Character, and List column types are supported. Columns containing Raw, Complex, or other R classes are not supported and will issue an error.

• Factors are now disallowed from grouping variables in multiset operations to avoid sort order discrepancies, and compatibility with factor handling in dplyr v.0.8.0. Factors will now be internally type-converted to character and a warning is issued.

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

valr documentation built on Sept. 19, 2023, 1:07 a.m.