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Use cpp11bigwig for read_bigwig() #425

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Jan 8, 2025
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Use cpp11bigwig for read_bigwig() #425

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Use cpp11bigwig for `read_bigwig()`
jayhesselberth Jan 7, 2025
5d64929
Update news
jayhesselberth Jan 7, 2025
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -21,6 +21,7 @@ Depends:
Imports:
broom,
cli,
cpp11bigwig,
dplyr (>= 0.8.0),
ggplot2,
lifecycle,
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43 changes: 23 additions & 20 deletions NEWS.md
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@@ -1,20 +1,23 @@
# valr (development version)

* `read_bigwig()` and `read_gtf()` were deprecated. The rtracklayer package used
for this functionality is no longer a dependency of valr due to errors from
* `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

* Address NOTE on CRAN about Rd link targets.
* Address NOTE on CRAN about Rd link targets.

* Change maintainer email address.
* Change maintainer email address.

# valr 0.8.1

* Make vdiffr dependency optional during package testing.
* Make vdiffr dependency optional during package testing.

# valr 0.8.0

Expand All @@ -26,17 +29,17 @@ CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.

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

# valr 0.6.6

Expand All @@ -49,15 +52,15 @@ CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.

# valr 0.6.5

* Handle `max_dist` for first intervals in `bed_cluster()` (#388)
* 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 intron score numbering error in `create_introns` (#377 @sheridar)

* Fixed bug in handling of list inputs for `bed_intersect()`(#380 @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)
* Added `read_bigwig` and `read_gtf` functions to import data into valr compatible tibbles (#379)

* Kent Riemondy is now maintainer.

Expand All @@ -69,7 +72,7 @@ CRAN AddressSantizer checks of the UCSC c-library code vendored in rtracklayer.

## Minor changes

* `RMariaDB` has replaced the deprecated `RMySQL` package as the database backend.
* `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.
Expand All @@ -84,17 +87,17 @@ but was masked by its Import by readr, which recently dropped use of Rcpp.

## Major changes

* `trbl_interval()` and `trbl_genome()` custom `tibble` subclasses have been deemed unnecessary and have been removed from the package.
* `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.
* 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`.
be suppressed by using `sorted = FALSE`.

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

Expand All @@ -108,13 +111,13 @@ be suppressed by using `sorted = FALSE`.

# valr 0.5.0

## Major changes
## Major changes

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

Expand Down Expand Up @@ -199,7 +202,7 @@ be suppressed by using `sorted = FALSE`.
## 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).
Expand Down
42 changes: 10 additions & 32 deletions R/read_bed.r
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Expand Up @@ -174,44 +174,22 @@ bed12_coltypes <- list(
)


#' Import and convert a bigwig file into a valr compatible tbl
#' Read a bigwig file into a valr compatible tbl
#'
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' This function will output a 5 column tibble with
#' zero-based chrom, start, end, score, and strand columns.
#' This function will output a 4 column tibble with
#' zero-based chrom, start, end, value columns.
#'
#' @param path path to bigWig file
#' @param set_strand strand to add to output (defaults to "+")
#'
#' @note This functions uses \code{rtracklayer} to import bigwigs which
#' has unstable support for the windows platform and therefore may error
#' for windows users (particularly for 32 bit window users).
#' @param ... params for `cpp11bigwig::read_bigwig()`
#'
#' @examples
#' \dontrun{
#' bw <- read_bigwig(valr_example("hg19.dnase1.bw"))
#' head(bw)
#' }
#' read_bigwig(valr_example("hg19.dnase1.bw"))
#'
#' read_bigwig(valr_example("hg19.dnase1.bw"), as = "GRanges")
#'
#' @export
read_bigwig <- function(path, set_strand = "+") {
lifecycle::deprecate_stop(
when = "0.8.3",
what = "read_bigwig()",
details = c(
x = paste0(
"read_bigwig() was removed because rtracklayer does not pass ",
"CRAN AddressSantizer checks of the UCSC C-library code vendored ",
"in rtracklayer."
),
i = paste0(
"use `bigWigToBedGraph` to convert bw to bedGraph,",
" and then `read_bedgraph()`. Alternatively use ",
"`rtracklayer::import()` then `gr_to_bed()`."
)
)
)
read_bigwig <- function(path, ...) {
cpp11bigwig::read_bigwig(path, ...)
}

#' Import and convert a GTF/GFF file into a valr compatible bed tbl format
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25 changes: 9 additions & 16 deletions man/read_bigwig.Rd
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5 changes: 2 additions & 3 deletions tests/testthat/test_read_bed.r
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Expand Up @@ -45,9 +45,8 @@ test_that("read broadPeak", {
})

test_that("read bigwig", {
skip_on_os("windows")
expect_error(read_bigwig(bigwig_path))
# expect_equal(ncol(x), 5)
x <- read_bigwig(bigwig_path)
expect_equal(ncol(x), 4)
})


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