v1.3.0

Features

• Breaking change: Most R functions have been moved to the chrombinarize R package which is now found in this repository (#2)
  • Tests are now available to show functions are working as expected
• Error messages spanning from shell scripts are now coloured red for readability (ANSI codes are used for this)

Refactors

• Renamed files stemming from processing WGBS and oxBS together (now just referred to as 5hmc files)
• File types are now more consistent across scripts thanks to (#2). All functions now take in 'bedmethyl', 'comparison_bedmethyl' or 'bin_counts' files.
• Many more checks are implemented when reading in files to avoid errors due to bad file format (with helpful error messages to explain why files are being rejected).
• The method for combining 5hmC and 5mC signals in bedmethyl files has been cleaned up.
  • Instead of relying on lead and lag functions, it instead extracts 5mC and 5hmC signals separately, then combines the two.

Fixes

• The method for finding the average methylation percent of surrounding/nearby CpGs is now faster and cleaner. It allows for more than 2 CpGs to be included in the average calculation (rather than the immediate neighbours being factored only).

Documentation

• Moved all documentation over to mkdocs (#1) for better organisation
  • Docs can now be found here
• Documentation for individual R functions are available upon loading the chrombinarize R package (provided by Roxygen)

Other (GitHub specific)

• Added CI for testing changes to R code
• Added badge to readme to show CI status
• Added contributing guidelines
• Added a PR template