Non-existant samples accepted by view

[jeromekelleher]

 python3 -m vcztools view performance/data/sim_10k.vcz/ -s NO_SAMPLE | head
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source=tskit 0.6.0
##contig=<ID=1,length=50818468>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##vcztools_viewCommand=view performance/data/sim_10k.vcz/ -s NO_SAMPLE; Date=2025-01-14 13:49:27.031019
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NO_SAMPLE
1       245     0       A       G       .       PASS    AC=0;AN=2       GT      0|0
1       427     1       A       C       .       PASS    AC=0;AN=2       GT      0|0
1       479     2       A       C       .       PASS    AC=0;AN=2       GT      0|0

correct output:

$ bcftools view performance/data/sim_10k.vcf.gz -s NO_SAMPLE
Error: subset called for sample that does not exist in header: "NO_SAMPLE". Use "--force-samples" to ignore this error.

[jeromekelleher]

Looking through the implementation and trying to replicate the above silent failure bug, it's not at all clear to me what's going on. I think the implementation needs to be decoupled from the CLI encoding (i.e. list of strings) and tested in isolation.

I think the best thing for us to ship a working version would be to disable the sample subsetting functionality at the front-end and return to it once that's done.