Use contig_id and filter_id arrays instead of attributes in write_vcf

[timothymillar]

Related to #1035. It looks like the code for write_vcf wasn't updated to use the new array variables (line). I also can't see "filter_id" in variables.py.

[hammer]

As more follow up on #1035: I see contig_id in variables.py but I don't see contig_id_spec in https://github.com/pystatgen/sgkit/blob/main/docs/api.rst. Maybe the latter file is only generated when we release? I don't know enough about how our docs are built to figure this out, but just wanted to point it out in case we need to do something to get contig_id in to the docs.