Arthur Rand

Hey @faulk-lab, I've implemented the ability to calculate entropy over user-defined regions. You can find the code on the `ar/entropy` branch and a build attached here. There are a few...

I fixed a few bugs and `--regions` now outputs the "window" bedgraph as well as the region summaries. [modkit_devb8f1f9ae_centos7_x86_64.tar.gz](https://github.com/nanoporetech/modkit/files/14949799/modkit_devb8f1f9ae_centos7_x86_64.tar.gz)

@faulk-lab Can you send me the error you get and a sample of the BED file?

Hello @lilypeck, There shouldn't be any changes in modkit v0.2.7 to v0.2.8 with respect to how the tabix index is handled. However, I did update the dependencies that `modkit` uses,...

Hello @lilypeck, I was able to reproduce the error using [noodles](https://github.com/zaeleus/noodles) version 0.69.0 (the version in modkit 0.2.8), the error does _not_ occur with version 0.50.0 (the version in modkit...

Hello @lilypeck, Alright, I've made a [branch](https://github.com/nanoporetech/modkit/tree/ar/gh-178) (build attached) where I've changed the version back. Please let me know if this build works. I'm going to investigate why the later...

@lilypeck Great, this fix is also in the 0.4.1 release.

Hello @ShokodkoMariia could you tell me what version of `modkit` you're using?

Hello @ShokodkoMariia, Sorry for the delay. Could you give me the exact commands you're using and whether or not they end up consuming excessive memory? Also could you tell me...

Hello @sahuno, In order to perform haplotype-specific methylation analysis, you'll need to use a phasing tool like [whatshap](https://whatshap.readthedocs.io/en/latest/) first. The output of this tool should be "haplotagged" reads where each...