Arthur Rand

Hello @kir1to455, > However, I found that the -t parameter of modkit does not use multiple CPUs to improve the speed of tasks. When you have a reference FASTA with...

Hello @kir1to455, The latest modkit release candidate [v0.2.5-rc1](https://github.com/nanoporetech/modkit/releases/tag/v0.2.5-rc1) should have much better performance when using a transcriptome reference. Let me know if you have a chance to try it and...

Hello @pkerbs, Could you tell me what version you are using? Version v0.2.2 had a large performance regression that was fixed in v0.2.3 onwards.

Hello @pkerbs, I see. The problem is probably due to the filtering algorithm, it is not optimized for many small regions like you have in your BED file. I appreciate...

Hello @ppapasaikas, I think you're hitting the known issue from above. What is the `--include-bed` you're using like? (i.e how many intervals, how long are they on average?). To get...

Hello @wdecoster, Yes this is something we can add. I'll try and get it into the next release. Happy to review a PR but no worries if you're busy.

Hello @OberonDixon, We've actually considered making a python wrapper/package around modkit, similar to what [modbam2bed](https://github.com/epi2me-labs/modbam2bed#python-package) had, but with extensions to all or most of the modkit functionality. This is probably...

Hello @OberonDixon, As far as your extract workflow. Make sure you have `v0.2.4` (or at least `v0.2.3`). There was a performance regression in `v0.2.2` that would make extract slow. In...

@OberonDixon Ah I see what you mean, the motif isn't a field in `extract`, sorry I missed that before. The motif is _technically_ in the `ref_kmer` field. We could add...

Hello @Ge0rges, For human-readable information such as the sample names, the place to look is the log file. The first line will always have the command itself, so any data...