vcztools query: optimize query evaluation

[Will-Tyler]

Description

With the --include and --exclude flags introduced in #82, users can filter variant sites for inclusion in the output. The current implementation evaluates the query for all of the variant sites, even if many of the variant sites are not selected by the filters. If no variant sites in a chunk are selected by the filters, an optimization can be made by not reading the chunk and not evaluating the query for those variant sites.

References

• bcftools query
• Query variant filtering #82

[Will-Tyler]

I think this task is much easier to implement with uniform chunk layouts (sgkit-dev/vcf-zarr-spec#22).

[jeromekelleher]

I think we can assume uniform chunk layouts. The best thing to do would be to raise an error in the bit of the code that's doing the query optimisation if the arrays its dealing with don't all have the required chunk layout.