Georges Kanaan

I can confirm the following error only occurs when both modified base models are used, in this case without specifying a batch or chunk size: ``` terminate called after throwing...

@wdecoster I'm wondering if this has been addressed further as I'm also interested in using what is now the official base caller's output (dorado) with your tool.

Seems like there's an issue reading the flyer output in this `try catch` block [here](https://github.com/katerinakazantseva/stRainy/blob/9d6a2d54315b9d84c0d059e5059d7093c275bffd/strainy/flye_consensus.py#L215C113-L215C129).

Apologies I was unaware of the status of RC releases.

Seems like I've run into this again on `v0.2.6`. Running the following command: ``` modkit dmr multi -s methylation_5/34h_assembly/top.bed.gz top -s methylation_5/34h_assembly/barcode01.bed.gz barcode01 -s methylation_5/34h_assembly/barcode02.bed.gz barcode02 -s methylation_5/34h_assembly/barcode03.bed.gz barcode03 -s...

Hi @ArtRand, I am indeed trying to do an all pairwise comparison in the context of a single site analysis. Is there a reason multi doesn't adopt package that loop?

Thanks @ArtRand! No worries about implementing that immediately, writing the loop is easy. I'm curious have you compared DMR results to the entropy feature?

Thank you for the prompt reply as usual. I would argue that the sample naming data should be within the file to make it more independent and less prone to...

@ArtRand which browsers are you thinking of when you say > the mixed delimiters are used so that the output is directly viewable with most commonly used genome viewers. In...

I wonder if the default output shouldn't be reverted to a tab-only bedmethyl file, with the adjusted format for genome viewers as a flag instead. The motivation here is that...