James Bonfield

Ah yes I see the PR (bedtools 620) with the big set of changes. Now is indeed the time to fix this. For now I'd say rename it to `cram_refs_t`...

I like this feature. Bar a few niggles, it looks solid. Thanks

Bumping this again to see where we're at. > I've removed bam_aux_remove2(), which was amongst other things a pain to use, and reunified bam_aux_remove() accordingly. (See force push to https://github.com/samtools/htslib/commit/99954c125b47166945a751b3a0d1fa20284b4cac...

Thanks. I did check if it was draft before commenting, as I had a recollection it was, but as you noted it's the samtools side that is the draft bit....

Thanks. I'll review the first couple commits with a view to merging them in isolation.

Hah beat me to it. I was going to squash and merge outside of this PR so as not to confuse your own branch (after testing it in anger with...

Yeah the draft sanitize function. We also discussed whether it belongs in htslib. My preference would be there and maybe enabled by an `hts_set_opt` call so any program can read...

Ah frogger-it... meant squash and merge rather than just rebase. Oh well, it is as it is :)

Could this be the same issue as https://github.com/samtools/samtools/issues/1622? Does it happen mainly after having been running for a while? Our assumption there is it is a connection timeout and that...

Ok, let's hope when we fix the other issue (ongoing) then your issues also get fixed. We'll let you know when a new version is available to test, or you...