NEWS

# bedr 1.1.2
==========================
- Add LICENSE.md to repository
- Update DESCRIPTION to include URL and BugReports links

# bedr 1.1.1
==========================
- Update CI/CD action
- Remove unnecessary package manual file

# bedr 1.1.0
==========================
- add vcf2bedpe module to convert structural variant calls obtained from Manta, GRIDSS and Delly v0.7.8


# bedr 1.0.7
==========================

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

# bedr 1.0.6
==========================

- updated support for tabix version >1.1. tabix deprecated option -B is now replaced with -R <regions file>

# bedr 1.0.5
==========================

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

# bedr 1.0.4
==========================

- Added rmarkdown in Suggests section
- Parameterised test.region.similarity() with gaps.file and repeats.file to support custom files
- 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
- Exposed utility function bed2index() via NAMESPACE to support its direct usage

# bedr 1.0.3
==========================

- 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
==========================

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

# bedr 1.0.1
==========================

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

# bedr 1.0.0
==========================

- Added bedr's first release