[RFC] Load graphs and paths in 'vg' format
Opened this issue · 2 comments
ekg commented
I don't think so. It's equivalent to GFA. So is the odgi format and other
custom indexes.
One thing that might help in reducing memory would be to load the GBZ
format. Then you get compressed paths in low memory. That's also equivalent
to GFA but then you're winning with the succinct data model.
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@ekg <https://github.com/ekg> Do you think it will be useful?
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asl commented
Well, it is equivalent, yes. However if things are already in 'vg' format then one would essentially skip the conversion from vg to GFA. Certainly it does not sense to support all plethora of possible custom formats here and there, however, I'm thinking that supporting few most widely used might improve the user experience.
We do support gzip-compressed GFAs now and after some recent improvements the memory consumption was significantly reduced, so I think we are ok so far. Unless you're having some examples where we might want to reduce memory consumption :)