VCF benchmarks

[tomwhite]

This is not ready for merging, but shows the current status of VCF read and write speed (#936 and #924).

sgkit/tests/io/vcf/test_vcf_benchmark.py::test_vcf_read_speed bytes read: 78683380
duration: 2.69 s
speed: 29.3 MB/s
PASSED
sgkit/tests/io/vcf/test_vcf_benchmark.py::test_vcf_write_speed [W::vcf_parse_format] Extreme FORMAT/AD value encountered and set to missing at 20:10000054
bytes written: 79602637
duration: 99.27 s
speed: 0.8 MB/s
PASSED

It should be possible to get both to ~100MB/s.

[tomwhite]

Re-running with the new code from #953, I get:

sgkit/tests/io/vcf/test_vcf_benchmark.py::test_vcf_write_speed bytes written: 81811189
duration: 0.84 s
speed: 97.7 MB/s
PASSED

This could be merged given that it only takes a few seconds to run now. It could be added to benchmark tests later (#938).

[jeromekelleher]

Do we want to put this in as a unit test? Maybe simpler to use have a vcf_benchmarks.py file in the root or something that you can run if you like? I don't really see the advantage of running this under pytest, since we also need benchmarks that definitely wouldn't run in seconds.

[tomwhite]

Yes, that's probably the best thing to do.

[tomwhite]

I've opened #976 as a replacement for this.

[tomwhite]

Closed in favour of #976