Sam Nicholls

I don't suppose anyone had a chance to look at this?

@alexcritschristoph Yes, we really ought to be using paired-end information better, and yup, `pysam` does given information on pairs. Not using this information is not a decision taken lightly and...

Although this is not desired behaviour, it is not high priority as it is off-label use of gretel.

Hi @jsgounot, thanks for the comment and I'm sorry about locking up all your storage! I don't intend to resolve this any time soon as Gretel is designed for local...

No problem - thanks for taking the time to report. Good luck!

Gretel is a proposal to the local MIH problem (defined in our manuscript here https://academic.oup.com/bioinformatics/article/37/10/1360/5988481) and is designed to find shorter regions of interest within metagenomic data. In theory it...

I thought I would try raising this myself, but it seems to linearly require more memory, meaning you must run fewer batches. This ends up taking much more GPU time...