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Changelog

Source: NEWS.md

valr (development version)

  • Eliminated all global variable dependencies by replacing bare column names with explicit .data[["column"]] syntax in data manipulation operations and all_of() in column selection operations.

  • Fixed bed_makewindows() step size calculation when step_size parameter is used. Previously, overlapping windows stepped by win_size - step_size instead of the specified step_size (#438).

  • Select methods (tibble, tribble) are now re-exported from the tibble package.

  • read_bigbed() is now re-exported from the cpp11bigwig package.

valr 0.8.4

CRAN release: 2025-06-22

  • Update a test for compatibility with forthcoming ggplot2 3.6.0 (#431)

valr 0.8.3

CRAN release: 2025-01-11

  • read_bigwig() now uses cpp11bigwig on CRAN. The set_strand param was removed to be more consistent with expected bigWig contents.

  • read_gtf() was deprecated. The rtracklayer package used for this functionality is no longer a dependency of valr due to errors from CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.

  • valr now depends on R >= 4.0.0.

valr 0.8.2

CRAN release: 2024-08-30

  • Address NOTE on CRAN about Rd link targets.

  • Change maintainer email address.

valr 0.8.1

CRAN release: 2024-04-22

  • Make vdiffr dependency optional during package testing.

valr 0.8.0

CRAN release: 2024-04-04

valr 0.7.0

CRAN release: 2023-09-18

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

valr 0.6.8

CRAN release: 2023-05-16

  • 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

CRAN release: 2023-02-18

  • 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

CRAN release: 2022-10-11

  • 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

CRAN release: 2022-08-19

valr 0.6.4

CRAN release: 2021-12-08

  • 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

CRAN release: 2021-05-15

  • Update to prepare for readr 2.0.0

valr 0.6.2

CRAN release: 2020-10-07

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

CRAN release: 2020-05-08

Bug Fixes

  • Fixed rchk unprotect error (#365)

valr 0.6.0

CRAN release: 2020-05-04

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

CRAN release: 2019-01-03

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

CRAN release: 2018-11-17

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

CRAN release: 2018-06-08

  • 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

CRAN release: 2018-01-25

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

CRAN release: 2017-07-22

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

valr 0.3.0

CRAN release: 2017-06-15

Enhancements

Bug fixes

valr 0.2.0

CRAN release: 2017-05-05

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

CRAN release: 2017-03-16

Major changes

Minor changes

Bug fixes

valr 0.1.1

CRAN release: 2016-12-01

Minor changes

  • test / vignette guards for Suggested RMySQL

  • fixed memory leak in absdist.cpp

  • fixed vignette entry names

valr 0.1.0

CRAN release: 2016-11-21

Major changes

  • initial release on CRAN