agalitsyna

HI, @ccoulombe Thanks for your PR! 1. Can you provide an example environment setting when the current version won't work? 2. How robust is setting the paths relative to $ORIGIN?

The simple solution is: (1) providing the screenshot of multiqc report html and (2) adding a disclaimer that it cannot be rendered as a part of the docs, but will...

Is it still relevant? For what modules?

To proceed with this idea further we need an example of what you mean by compression/decompression and how it may fail.

What we already have in bioframe and what might be useful for the discussion. - **filtering bin table by viewframe** has at least three bioframe-ish solutions: 1. bioframe.select with pd.concat...

1) The solution above changes the names from "upstream/downstream" to "left/right", which is inconsistent across bioframe tools, e.g., in `closest`, we have this definition of [upstream/downstream](https://github.com/open2c/bioframe/blob/main/docs/tutorials/tutorial_assign_peaks_to_genes.ipynb). The reasoning for separating...

I think that with the emergence of jupyter walkthrough, it's not needed anymore: https://github.com/open2c/pairtools/blob/pre0.4.0/examples/pairtools_walkthrough.ipynb My proposal is to remove the example_pipelines completely. Jupyter walkthrough and docs provides enough explanation and...

@Phlya Is it fixed now?

With recent update, we have a whole-pairtools logging, we can add it there: https://github.com/open2c/pairtools/pull/117 For that, we need an example the unmapped sam entry can be encountered and result in...

I believe your contact pairs have non-typical encoding of mapq. What mapper/version did you use? We usually use bwa mem output, and its mapq is integer. That's the first time...