Sensible handling of BAMs larger than 50K reads

[mattloose]

Currentyl little john explicitly skips bams with more than 50K reads. We need to handle this transparently to the user and let them know about the issue.

We could also optionally handle this, although little john is designed to handle small batch streaming data.

[felixphd2025]

Hello - I have ~10 oxford nanopore runs on paed brain tumour samples using the ligation kit. I was wondering if you had a recommended script to potentially convert the larger bams into ~25k read bams.

I've made a rudimentary samstools script but i am concerned that this is generating duplicated reads. for example bam 1 of ~100k reads gets split into 4 x 25k reads. it will then do this for all the individual bam files from the output run.

How do you recommend I do this and do you have your own "validated" code you would be willing to share.

Alternatively I could use the old version of robin for now.

thanks so much!

felix