vgteam
vg paths (and other graph-modifying tools) should convert to mutable formats automatically
In https://github.com/vgteam/vg/issues/4568#issuecomment-2814148353 someone got a message that vg couldn't do something because their GBZ graph wasn't mutable.
We should find all the places where we bail out because a graph can't be modified, and replace them with conversions to mutable formats (or maybe a mutability overlay?) so tha tthe user doesn't need to deal with this.
The message as is is unhelpful because it provides no indication of whether this is what GATK loves to call a USER ERROR or whether something has gone wrong internally, and it also provides no advice as to how one might obtain a mutable version of a graph.
Just chiming in to add the suggestion that it would be useful for bgzipped gfa files to be accepted.
It is maybe not such a big deal, but still inconvenience since uncompressing the (for instance) 8 GB hprc-v1.1-mc-grch38.gfa.gz takes many minutes and creates a 45 GB file.
