vcztools query: support looping over samples

[Will-Tyler]

Description

This task is to support format fields in the vcztool query CLI. Format fields must be enclosed in square brackets to loop over all the samples. vcztools query is based on bcftools query.

The -f option in vcztools query was added in #64.

Example

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

This example from bcftools query illustrates using square brackets to print the sample ID, %SAMPLE, and the genotype, %GT, for all samples. We want to support this functionality in vcztools query as well.

References

• bcftools query
• Query format #64
  • This pull request adds the -f option to vcztools query.

[jeromekelleher]

This sounds great @Will-Tyler! Just to note that this is definitely a case where we'd want to pre-filter before fetching data from Zarr, unless the bcftools semantics bars us from doing so.