NEWS.md

In uclahs-cds/public-R-bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

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• Replace outdated autostart in fread with skip.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

• Update CI/CD action

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

• Initial release

uclahs-cds/public-R-bedr documentation built on June 1, 2025, 10:21 p.m.