James Bonfield

I managed to reproduce this by generating a SAM header with 40 million lines, but no M5 strings, and then converting this to CRAM. The crash was simply because it...

There were a lot of changes to mpileup. See the release notes in https://github.com/samtools/bcftools/releases/tag/1.13. You may be able to just add `--config 1.12` when using 1.15 to get the old...

At the GA4GH discussion someone raised the thought about linkage to external files. That sounds like a far better solution. The ability to be able to specify related files somewhere...

Rebased off current master, with the line-wrapping adjusted for SAMv1.tex. The "phred-true-scale" sentence has been rewritten as left in as a separate commit so you can see the change, but...

Applied the changes to VCF4.4 draft and, minimally to VCF4.2. I also squashed the previous commit and this change into the main VCF doc updates. For review purposes the changes...

I fixed the `log` vs `\log` comment in two new commits, with the first best squashed. I don't know if it needs squashing down or up though! (Or maybe all...

Did you mean `@16`? The option should be `-@16`. Is it actually using CPU time, or has it bizarrely got confused and is waiting on stdin or something silly. "top"...

I'm hoping the definition of what's valid and how to deal with invalid chars is compatible between CRAM (edit: actually SAM) and RefGet (I'm sure they must be given the...

When you say "similar to", do you mean "identical to"? I think all of the statements you list are true if we do this conversion, so a workaround exists currently....

Aux tags can as we have the ability to process all of them (at least once https://github.com/samtools/samtools/pull/1679 lands). PG/RG header info is problematic though. It needs some reheader hackery. Maybe...