switch BGZFStreams for BGZFLib

[jonathanBieler]

I had some time so I've tried to replace BGZFStreams the new libdefalte based BGZFLib. I used Claude for this but it was struggling quite a bit so I also had to contribute as well... The code look ok I think and all tests pass. There's maybe some rough edges (e.g. _to_virtual_offset should be a method in BGZFLib?) but maybe that can be tackled later on, using this PR as a base.

I also added to methods for allocation free sequence and quality extraction.

The performance are pretty good, computing the mean base quality on a 3.0G BAM file, 3x faster, same result :

Before :

29.076704 seconds (2.61 M allocations: 180.409 MiB, 0.10% gc time)
39.3092853294488

After :

10.851930 seconds (3.68 M allocations: 256.426 MiB, 0.31% gc time, 85932 lock conflicts)
39.3092853294488

[jakobnissen]

This is very exciting! I'll look at it one of the following days when I get time. Some changes might need to be upstreamed to BufferIO.jl or BGZFLib.jl (I'll handle that).

I would prefer the PR is split into one which solely switches the BGZF library.
Could you (perhaps using a coding agent) focus this PR to only include the switching of the underlying BGZF library, and then make another PR, possibly built on top of this one, which adds the new features?

[jonathanBieler]

Done, it was easy to separate. I added these to try to reduce allocations to a minimum, I think the BGZFLib version allocates a bit more than BGZFStreams.

[kescobo]

Not ideal to lose the current LTS, but I don't think it's a dealbreaker

[jonathanBieler]

I think it's MemoryViews that requires 1.11

[jakobnissen]

Let me know if you need any help with the PR or implementation

[jonathanBieler]

I did another pass on this, benchmark still looks good, it allocates more but it's because I'm using the sequence and qualities :

12.025843 seconds (196.71 M allocations: 18.897 GiB, 24.67% gc time, 1953 lock conflicts, 0.26% compilation time)
[ Info: 39.3092853294488

[jakobnissen]

I think you're almost done! Just two more bugs I found - then it can be merged.

[jakobnissen]

Thank you!