To make it a bit more concrete. cooler cload pairix calls the query2D method of the pairix file instance with the size of the whole chromosome and later uses the returned iterator to fetch pairs from up to 5 chunks the chromosome is divided into.

Honestly, I'm not sure what the repercussions are. I would try querying the pairs file directly with pairix using out-of-bounds coordinates and see what it does or wait to hear back from the pairix maintainers.

I'm curious, would plain old cload pairs (not pairix) not work in your case? It does a two-pass ingestion using mergesort without requiring an index or even sorted pairs. Or do you run into performance issues?

Meant to post that in the cooler issue, but whatevs...

Yes, I already thought about the out-of-bounds querying and wanted to try it today, but didn't manage to. However, I will do so tomorrow and let you know.

As far as I can remember I never tried to use cload pairs because we decided to go with pairix due to the nice querying with pypairix, but I will also look into this.

Thanks anyway

I'll have to modify pairix to add an option to increase max chrom size. Just curious, what specie is it?

Thanks for moving so quickly. It's axolotl and it defies every heuristic you have learned for processing genomic data ^^

That's cool! I'll take a look at it next couple of days and let you know.

I also leave this here:
querying ranges outside the MAX_CHR threshold does not return any pairs from the file and thus the resulting matrices are empty in regions above MAX_CHR. cooler cload pairs is a convenient workaround for this for now. Thanks for the help