Erik Garrison

Sorry that it's hard to run. FWIW, We are rewriting based on waragraph to simplify the GPU related dependencies. But if you have a chance please share your errors with...

Yup, it's awkward as a dependency, but Vulkan is what allows gfaestus to provide zoomable views of whole chromosome pangenome graphs with base-level variation. The rewrite in the works rebuilds...

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...

Sure! The basic idea is that any path range, e.g. BED interval in a FASTA sequence space corresponding to the path space of the graph, can be converted into a...

The main problem is storage of the graph in memory. I would suggest switching to a library based on succinct data structures. Libhandlegraph and odgi both have suitable implementations. These...

It's not just about putting it in memory, but about providing efficient random access to its parts. The paths are particularly ruinous in this regard. You can have fast path...

I see, you're totally right! Alternatives are odgi and libhandlegraph. The PackedGraph model is especially efficient.

Sorry, specifically you'll want libbdsg: https://github.com/vgteam/libbdsg. libhandlegraph is an abstract interface in C++, not an implementation.

Adding overlap lengths to the link lines would be the missing part, otherwise I think it should be more directly applicable to generic GFAs that gbwtgraph.

Path position queries: find me the node at a given path position. Given a node, what path positions is it at (or near). On Wed, Sep 22, 2021, 06:13 Anton...