bedr 1.1.3 (2025-04-04)
Added
- Add
method argument to in.region
function
Changed
- Update changelog to Markdown
NEWS.md format
- Use updated
renv GitHub action for
R CMD check
- Rename internal helper function
parse.vcf.header() to
prep.vcf.header() to avoid naming conflict with base R
parse() S3 method.
Fixed
- Replace outdated
autostart in fread with
skip.
- Fix cross-reference format in manual
- Update GitHub links
bedr 1.1.2 (2024-01-24)
Added
- Add LICENSE.md to repository
- Update DESCRIPTION to include URL and BugReports links
bedr 1.1.1 (2023-08-24)
Changed
Removed
- Remove unnecessary package manual file
bedr 1.1.0 (2022-03-01)
Added
- Add vcf2bedpe module to convert structural variant calls obtained
from Manta, GRIDSS and Delly v0.7.8
bedr 1.0.7 (2019-04-01)
Changed
- forced vcf2bed not to print genomic coordinates in R scientific
notation for interoperability with other processors
bedr 1.0.6 (2019-01-12)
Fixed
- Updated support for tabix version >1.1. tabix deprecated option
-B is now replaced with -R
bedr 1.0.5
Fixed
- fixed incorrect ordering of chromosome table returned by
get.chr.length() - [rolled back]
bedr 1.0.4 (2017-10-12)
Changed
- Added rmarkdown in Suggests section
- Parameterised test.region.similarity() with gaps.file and
repeats.file to support custom files
- Exposed utility function bed2index() via NAMESPACE to support its
direct usage
Fixed
- Fixed bug when bedtools ‘coverage’ output is post-processed in
bedr
- Fixed is.valid.seq() to comply with inputs and outputs as described
in docs
bedr 1.0.3 (2016-08-23)
Changed
- Standardised function name; renamed snm() to bedr.snm.region()
- Listed SystemRequirements to the package metadata
- Added support for Human hg38 genome assembly
bedr 1.0.2 (2015-09-21)
Fixed
- Fixed compatibility with data.table >= v1.9.6 for
data.table::fread() call
bedr 1.0.1 (2015-09-05)
Fixed
- Fixed sort –version command as Solaris does not support –version
which is GNU specific
bedr 1.0.0 (2015-09-03)
Added