vg call strips path/contig info from vcf

[CormacKinsella]

1. What were you trying to do?

• Produce a VCF from a mapped GAM

vg call graph.gbz --pack graph.pack --snarls graph.snarls --genotype-snarls --all-snarls --gbz-translation --gbz  > example.vcf

2. What did you want to happen?

• I expected the VCF #CHROM column to retain the full contig/path name (which is in PanSN format), like the behaviour of vg deconstruct. e.g.:

#CHROM
simChimp#0#simChimp.chr6

3. What actually happened?

• It stripped out the other info in the contig name, leaving the below
• This means I can't pipe the vcf further into bcftools for normalisation vs the reference.fasta

#CHROM 
simChimp.chr6

5. What data and command can the vg dev team use to make the problem happen?

I did this using the simChimp example from Minigraph-Cactus, but I assume any gbz with PanSN contig naming.

6. What does running vg version say?

v1.61.0 "Plodio"

[CormacKinsella]

I think this may be the same issue as #4442. I assumed I could run vg call without specifying a reference sample with -S (for a graph with only one ref sample), as according to the -p readme it should default to all reference paths

-p, --ref-path NAME Reference path to call on (multipile allowed. defaults to all paths)

Cheers for any advice!