setGT problem with phased genotypes

[VLoegler]

Hi,

I'm using setGT to change half missing genotypes (./1) to fully missing genotypes. The problem is that I have some phased genotypes (ex: 0|. 2|.) and setGT doesn't handle these one.

Here is the command I used:

bcftools +setGT -- -t ./x -n .

The possibility to have -t .|x would be very useful.

[pd3]

The usage page suggests that both phased and unphased half-missing genotypes are supported

./x  .. partially missing (e.g., "./0" or ".|1" but not "./.")

however, it turns out that was not the case.

The bug is now fixed, thanks for reporting the issue.