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vgteam / libhandlegraph

Library for the Handle Graph abstraction
MIT License
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Optimize method for mutable handle graph #10

Closed jeizenga closed 5 years ago

jeizenga commented 5 years ago

I have an interface that that allows a semantically unspecified optimization step for the representation of a graph. I think this is general enough to handle the sorting methods we discussed earlier, as well as other potential optimizations we might want to make to the data structure.

I also thew in methods for get_base and get_subsequence with default implementations. Those seem handy.

ekg commented 5 years ago

This is a fine way to set up a high level interface to allow the compaction or reorganization of the graph in various ways that the implementer knows will help performance.

I still think we need to be able to maintain an order in the graph. There are a number of algorithms that I'd like to be able to run on many handle graph implementations, but won't be able to if I can't define a stable ordering that gets serialized and doesn't need to be re-derived every time the graph is loaded. My point is that this would be a good thing to promote in the handlegraph interface.

I'll make a new PR for this.

jeizenga commented 5 years ago

I believe I should have fixed the include order dependence (https://github.com/vgteam/libhandlegraph/issues/11) with the last commit.