James Bonfield

> However, it does look like sometimes the forward strand of a read pair is used and other times the reverse strand. This is what I really meant when I...

Note this requires https://github.com/samtools/htslib/pull/1771 merging first due to additional htslib APIs being added.

Ping @mcshane. Please check if the syntax and functionality for this works for you as a replacement to io_lib's filtering. Thanks

I thought the same. I've sometimes wondered if we should move all the old sourceforge releases sideways into a subdirectory, to deliberately break all those ancient legacy pipelines that still...

For validation, I've just been doing some perl one-liner hackery to summarise the samtools view outputs. Eg: ``` samtools sort -Osam -n test.sam | perl -ane 'next if /^@/; next...

Your develop is way behind. Please update so you can then rebase it. A lot of the test failures are elsewhere in samtools, but have been fixed already.

Regarding the functionality, I'm tackling this from a different direction and this is ongoing work that's likely to land in a PR soon. - Base-callers emit MM/ML tags - Aligners...

> Also are MN tags specified anywhere? I can't find them on hts-spec's samtags? Yes, as a PR that really needs some traction: https://github.com/samtools/hts-specs/pull/714

> Thanks James. I've just been looking at your fixmate_MM branch and I think I might be able to reuse a few of your functions to trim MM tags. Maybe...

I thought we'd merged that already, but looking back it was `samtools view -d` (042d9db4e6ec4abb2cba39d83c2e7d258bf5fe36). https://github.com/samtools/samtools/pull/1934 added the -d option to split, so I agree it ought to follow the...