Arthur Rand

Hello @Ge0rges, @jrobinso , The motivation to use the mixed-delimiter output in modkit was to allow the output bedMethyl files to be directly loaded into browsers such as IGV. When...

@jrobinso, Sounds good. My assumption was that by using spaces IGV was effectively ignoring the extra information. I'm very excited for the `.bedmethyl` extension, as you can imagine accessible interoperable...

@jrobinso try the file attached, generated by the released version of modkit using the `--only-tabs` flag. [duplex-tabs.bed.zip](https://github.com/nanoporetech/modkit/files/12719663/duplex-tabs.bed.zip). It should correspond to GRCh38. Of course I had to zip it because...

@jrobinso, Great, happy to help iterate. I'll start testing with the web version too.

The latest snapshot of IGV desktop supports the current and `--only-tabs` version of modkit output. It would be potentially an API-breaking change but modkit could make `--only-tabs` the default in...

As of version 0.3.0 the bedmethyl output uses only tabs, I've tested on IGV 2.17.4 and it parses the data as expected.

@NickNCL One thing you could do is run ``` mkdir -p ${out_dir} modkit sample-probs ${your_bam} --hist --out-dir ${out_dir}` ``` Then inspect probabilities.txt and probabilities.tsv and set the threshold manually with...

Hello @Ge0rges, You can, there is a one-liner below. Do you want to know the distribution of probabilities when the samples are combined? Using a combination of `sample-probs` and `extract`...

Hello @jcolicchio-soundag, Could you tell me a little more about the compute environment you have, which processor architecture are you on? Which version of cargo and cmake? Could you show...

@jcolicchio-soundag That's certainly perplexing. Would it be at all possible for you to share the file with me so I can try and reproduce the problem? Looks like you're running...