Jordan Eizenga

I think I used a minimum MAPQ of 30, which is a pretty standard threshold for a confidently mapped read (it corresponds to an estimated probability of error of 0.1%)....

Could you also provide the `vg mpmap` command you used?

You can send material to [email protected]. Just to be clear: is this a separate issue from the one posted above by @abcyulongwang ?

Are you able to share the inputs that led to the crash?

Are you able to share the data that led to this crash?

It looks like you are providing multiple graphs to `vg snarls`. Is that correct? If so, it could be that your graphs don't have disjoint node IDs. It might also...

I think the issue is that you're only extracting the path itself and not the non-reference variants. If you want to use `vg find` for this, you should also specify...

Regarding `vg prune`, I've had a look and I think that this is expected behavior. The `vg prune` algorithm is meant as a preprocessing step for creating a GCSA2 index,...

It will also extract all of the nodes that you can reach from the path by following `STEPS` edges from one of the nodes on the paths. It's a bit...

That's a common point of confusion. It's basically for algorithmic convenience. In several places, we have a hard limit of 1023 bases because we only use 10 bits to express...