v1.2.0

Features

• [BREAKING CHANGE]: Software requirements have been slashed. New build process has been implemented that uses conda and the R package renv. This in principle allows for more portability and reduces prerequisites for running the scripts.
• Added an option to use only CpG sites that are in CpG islands when fitting the binomial distribution to erroneous read probability.
  • This is possibly less desirable for ONT data where base calling might be affected by CpG density. It is more likely to be useful for BS-Seq data
  • This step is optional in case you cannot obtain a CpG island reference for your dataset (hg19 and hg38 are provided for you)
• Added a script that allows the user to convert a binary file from one bin size to another (useful with datasets with multiple modalities)
• [BREAKING CHANGE]: Changed method for determining densely methylated CpG sites. New method uses density information with the beta distribution rather than frequency/count information with the Poisson distribution.
  • This will work nicer with more varied bin sizes.
  • Changed log file locations to be more structured (sorted by job name and user)
  • Changed some default values in the config-setup file

Refactors

• Moved parameters back into config file (keeping all configuration in one file is easier)
• Renamed some files to be more informative of what they do
• Moved end location of sparse and dense binary files to make it easier to use ChromHMM's MergeBinary command
• Removed obsolete Rscript that installed R libraries (in favour of renv)