[query] bad error message when user needs to use array_elements_required=False about hail HOT 2 CLOSED

I asked for some clarity from the VCF spec on what . means so that we can possibly be less pedantic.

samtools/hts-specs#737

from hail.

I have an RFC proposal to just handle the ambiguity: https://github.com/hail-is/hail-rfcs/blob/main/rfc/0008-handle-vcf-array-field-ambiguity

I proposed a PR to fix this: #13465 However, I missed a key issue: many VCF's elide fields to indicate missingness. That is not ambiguous: a field that is entirely elided is clearly missing, not an array of one missing value. You can't do this in a FORMAT (aka entry aka genotype) field, but you can do this in an INFO field a la:

##fileformat=VCFv4.2
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=NUMS,Number=*,Type=Float,Description="some numbers">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT ...
... AC=1,1;AN=1 ...

the NUMS field should be read as missing. My PR considered it unacceptably ambiguous because it thought it had been NUMS=..

I don't think we can fix this problem entirely from Python. We need to use Scala-side logic because after we parse in Scala, we lose the knowledge that a field was entirely elided versus a single missing dot.

from hail.