Changes in version 1.1.5 (2026-01-24)                  

Changed

  - Update maintainer email to pboutros@sbpdiscovery.org
  - Update GitHub organization from uclahs-cds to theboutroslab
  - Rename repository from public-R-bedr to package-bedr

                        Changes in version 1.1.4                        

Changed

  - Use updated R CMD check CI/CD action.

                 Changes in version 1.1.3 (2025-04-06)                  

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  - Replace outdated autostart in fread with skip.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

                        Changes in version 1.1.2                        

Added

  - Add LICENSE.md to repository
  - Update DESCRIPTION to include URL and BugReports links

                        Changes in version 1.1.1                        

Changed

  - Update CI/CD action

Removed

  - Remove unnecessary package manual file

                        Changes in version 1.1.0                        

Added

  - Add vcf2bedpe module to convert structural variant calls obtained
    from Manta, GRIDSS and Delly v0.7.8

                 Changes in version 1.0.7 (2019-04-01)                  

Changed

  - forced vcf2bed not to print genomic coordinates in R scientific
    notation for interoperability with other processors

                 Changes in version 1.0.6 (2019-01-12)                  

Fixed

  - Updated support for tabix version >1.1. tabix deprecated option -B
    is now replaced with -R 

                        Changes in version 1.0.5                        

Fixed

  - fixed incorrect ordering of chromosome table returned by
    get.chr.length() - [rolled back]

                 Changes in version 1.0.4 (2017-10-13)                  

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

                 Changes in version 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

                 Changes in version 1.0.2 (2015-09-21)                  

Fixed

  - Fixed compatibility with data.table >= v1.9.6 for
    data.table::fread() call

                 Changes in version 1.0.1 (2015-09-05)                  

Fixed

  - Fixed sort --version command as Solaris does not support --version
    which is GNU specific

                 Changes in version 1.0.0 (2015-09-04)                  

Added

  - Initial release