Changelog
Source:NEWS.md
valr 0.8.0
CRAN release: 2024-04-04
- Added
bed_genomecov()
to compute interval coverage across a genome.
valr 0.7.0
CRAN release: 2023-09-18
-
read_bed
and related functions now automatically calculate the fields. Use ofn_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 withNA
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 inbed_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 fromx
with no matching group iny
(#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 tobed_makewindows()
was removed.
valr 0.6.0
CRAN release: 2020-05-04
Major changes
trbl_interval()
andtrbl_genome()
customtibble
subclasses have been deemed unnecessary and have been removed from the package.coercing
GRanges
to avalr
compatible data.frame now uses thegr_to_bed()
function rather thanas.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 ofbed_random()
has been changed tosorted
, and will now by default usebed_sort()
to sort the output, rather than rely on naming the sorting columns. Sorting can be suppressed by usingsorted = FALSE
.bed_sort()
now uses base R sorting with theradix
method for increased speed. (#353)tbls
processed bybed_merge()
orbed_sort()
no longer store eithermerged
orsorted
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 they
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 ondplyr
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 callas_tibble()
only on non-tibble input, which prevents groups from being stripped fromtibble()
input (#338).
valr 0.4.1
CRAN release: 2018-06-08
Added new function,
bed_partition()
, which is similar tobed_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 inbed_partition()
and timings invignette('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 invignette('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 internalintersect_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 inmakewindows_impl()
(#312 @kriemo)
Bug fixes
Fixed off by one error in reported distances from
bed_closest()
. Distances reported now are the same asbedtools closest
behavior (#311).bed_glyph()
acceptstrbl_intervals
named other thanx
andy
(#318).bed_makewindows()
now returns the number of windows specified bynum_win
when the input intervals are not evenly divisble intonum_win
, consistent withbedtools
behavior.The output of
findOverlaps()
is now sorted insubtract_impl()
to prevent reporting intervals that should have been dropped when callingbed_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()
convertsGenomicRanges::GRanges
objects totbl_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 reducearrange
calls in library code.
Bug fixes
-
bed_merge()
now reports start/end columns if spec is provided (#288)
valr 0.3.0
CRAN release: 2017-06-15
Enhancements
New
create_introns()
,create_utrs5()
andcreate_utrs3()
functions for generating features from BED12 files.Speed-ups in
bed_makewindows()
(~50x),bed_merge()
(~4x), andbed_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
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()
andtbl_genome()
that wrap tibbles and enforce strict column naming.trbl_interval()
andtrbl_genome()
are constructors that taketibble::tribble()
formatting andis.tbl_interval()
andis.tbl_genome()
are used to check for valid classes.
Minor changes
- intervals returned from
bed_random()
are sorted bychrom
andstart
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
- Deprecate
bed_sort()
in favor of usingdplyr::arrange()
explicitly (fixes #134).
Minor changes
add
src/init.c
that callsR_registerRoutines
andR_useDynamicSymbols
to address NOTE in r-develDeprecate
dist
parameter inbed_closest()
in favor of using user supplied functions (#182 @kriemo)Make
.id
values sequential across chroms inbed_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)