libhandlegraph
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vgteam
Library for the Handle Graph abstraction
This changes the notation for subpaths, and adds some queries related to "scaffolds" that paths are on. It also eliminates phase blocks. We are going to use possibly-fake coordinate ranges...
`VectorizableHandleGraph::edge_index` should state that the edge_t has to be from `for_each_edge`or `edge_handle` (i.e. in canonical order and orientation).
Hi, I am trying to use the dijkstra algorithm defined in `libhandlegraph` but getting a linker error. ```` undefined reference to `handlegraph::algorithms::dijkstra(handlegraph::HandleGraph const*, handlegraph::handle_t, std::function, bool)' ```` There are not...
The current handlegraph api, uses the internal iterator approach (e.g. `for_each_edge` etc.) This is very inconvenient when trying to use this code from python. The only way to move data...
In order to use the RankedHandleGraph interface on a PathHandleGraph, we need to either derive a new class, a RankedPathHandleGraph, or use a dynamic cast. These are kind of common...
An important operation is to remove nodes from the graph. For instance, we might want to remove low-coverage nodes. This can cause us to remove nodes in the middle of...
It would be useful if we had a standard way to assign and obtain non-numeric node names. This would be an optional trait, like the serialization or vectorization interface. It's...
Ensuring that edges aren't duplicated can require linear-time operations (in the number of edges). For graphs with some nodes that have very high degree, this quickly becomes a problem. I...
An example of a null handle as proposed in #22. I think this is handy, especially when re-working existing code that may rely on checks of the form `Node* ==...
I'd like to match divide_handle with an inverse function that combines handles back together. This would be the signature: ```c++ handle_t combine_handles(const std::vector& handles); ``` Any thoughts?