I think this language could be slightly clearer. What I meant to say in my previous comment was that in the abstract, residue- and inter-residue coordinates can both be 0- or 1-indexed. I think what we're saying here is that the RESIDUE enum value means "1-indexed residue" and INTER_RESIDUE means "0-indexed inter-residue". Feel free to edit further but I think we should have this line say something like
``RESIDUE`` means 1-indexed, residue coordinates and ``INTER_RESIDUE`` means 0-indexed, inter-residue coordinates.
I also think we should probably have a note about this in the "usage" section of the docs -- feel free to make a new issue + assign me if you agree
I also think we should probably have a note about this in the "usage" section of the docs -- feel free to make a new issue + assign me if you agree
_Originally posted by @jsstevenson in https://github.com/GenomicMedLab/cool-seq-tool/pull/337#discussion_r1698969286_