"bcf_synced_reader.h:108 operator()" error wen using vt sort

[estolle]

Hi there

I was running an older script which previously worked, but now threw an error at the step when I use vt sort on a VCF file:

vt sort $TF/test2.vcf
[E:bcf_synced_reader.h:108 operator()] alleles not defined in VCF record.
There is nothing I found being wrong with the VCF, I changed headers, sorted, checked alleles and genotypes, tested on subsets and other VCFs. It always comes up for a reason unclear to me.

Seems its similar to this issue:
DecodeGenetics/graphtyper-pipelines#3 (comment)
This describes that an older version works (and that commit fixed some htslib stuff). Indeed I never changed the previously working vt installation (vt v0.57721) but I updated htslib. So perhaps the problem is related to that.

Other tools work:
bcftools sort -Ov $TF/test2.vcf
no error

vcfstreamsort -a $TF/test2.vcf
no error

vt validate $TF/test2.vcf or vt peek $TF/test2.vcf work as expected too.

In the meantime I am using bcftools or vcflib to sort the vcf, but perhaps the issue in vt can be fixed.