Work around glnexus issue

[holtgrewe]

Is your feature request related to a problem? Please describe.
In #356, we added a script to fix glnexus output for Mehari.
zaeleus/noodles#235 now recommends a fix to our code directly.

Describe the solution you'd like
Apply the fix so we don't need the preprocessing step.

Describe alternatives you've considered
N/A

Additional context
N/A