Bug in VCF output when selected samples have all missing GTs.

[jeromekelleher]

vcztools drops FORMAT fields with missing values when subsetting samples, instead of emitting . placeholders like bcftools

When subsetting chr22.vcf.gz to a single sample (-s HG00096), vcztools omits FORMAT fields where the selected sample has no data, while bcftools retains them with . placeholders.

  bcftools:  GT:AD:DP:GQ:PL     ./.:0,0:0:.:.                                                                                                                                       
  vcztools:  AD:DP      0,0:0                                     

This causes downstream tools (e.g. cyvcf2) to fail when they expect GT to be present.

I think this is a bug, because we can't have AD/DP with no GT.

[percyfal]

I'm hitting this in a slightly different scenario in which I in a VCZ archive set call_genotype values to -1 (missing) based on coverage thresholds. In some cases this leads to missing genotype calls for all samples. Simply removing the if statement in formats.c#L689 does the trick on a simple test case.

[jeromekelleher]

Thanks @percyfal - I'll roll a fix for this into the next batch up updates