output two dots for empty GT values

[aryarm]

in some cases, HipSTR will output a GT value of .

but it should output ./. instead, according to the VCF spec:

If a call cannot be made for a sample at a given locus, ‘.’ must be specified for each missing allele in the GT field (for example
‘./.’ for a diploid genotype and ‘.’ for haploid genotype).

This might be the line of code where this happens:

HipSTR/src/seq_stutter_genotyper.cpp

Line 1318 in ef22e89

empty_gt << ".:";

[yli091230]

Hi Arya,
Thanks for the note. I noticed the same issue but didn't check the code. I'll fix the code.

[aryarm]

oooh, thanks for offering to do that, @yli091230 !

@mlamkin7 , would you happen to have a bam or cram file that @yli091230 could use to replicate the issue for a test?