High-Performance Open-Source Archive
bed_slop() and bed_flank() now preserve
input row order instead of sorting output by chrom and
start (#434, #435).
Fixed bed_closest() to respect custom
suffix parameter when computing .dist column
(#436).
Improved memory efficiency in bed_intersect() by
using a visitor pattern, reducing allocations for large datasets
(#446).
min_overlap parameter to
bed_intersect(), bed_subtract(),
bed_coverage(), and bed_map(). The default
min_overlap = 1L aligns with bedtools behavior where
book-ended (adjacent) intervals are not considered
overlapping. Use min_overlap = 0L to preserve the previous
valr behavior where book-ended intervals were treated as overlapping.
Currently, calling these functions without an explicit
min_overlap value will emit a deprecation warning and use
the legacy behavior (min_overlap = 0L). In a future
release, the default will change to min_overlap = 1L, so
users should update their code to explicitly specify the desired
behavior.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.
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.
Address NOTE on CRAN about Rd link targets.
Change maintainer email address.
bed_genomecov() to compute interval coverage
across a genome.read_bed and related functions now automatically
calculate the fields. Use of n_fields was deprecated.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).
Removed SystemRequirements from DESCRIPTION to
eliminate a NOTE on CRAN.
bed_coverage() now reports intervals from
x with no matching group in y (#395).
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.
max_dist for first intervals in
bed_cluster() (#388)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.
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.
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.
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.
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)
Rcpp functions have been reorganized to remove
all dependencies on dplyr C++ functions.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.
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 https://github.com/rnabioco/valr, update links and docs.
Move shiny app to new repo (https://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
Need mirroring services?
Contact our team at info@vpspulse.com.
Mirror powered by VPSpulse
Infrastructure sponsored by VPSPulse & Secure Payments by ArionPay.