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A D library for computational biology and bioinformatics
Home Page: https://biod.github.io/
License: MIT License
This project forked from biod/biod
A D library for computational biology and bioinformatics
Home Page: https://biod.github.io/
License: MIT License
Add the Burrows Wheeler Transform to BioD.
Implementation plan:
Add a template for standardizing the reporting of issues the repository.
Add templates for:
We should have graph support in BioD but we don't yet.
Implement a graph as an adjacency matrix
Implementing a graph as an adjacency list
Because the adjacency-list representation provides a compact way to represent sparse graphs—those for which |E| is much less than |V|2—it is usually the method of choice. Most of the graph algorithms presented in this book assume that an input graph is represented in adjacency- list form. We may prefer an adjacency-matrix representation, however, when the graph is dense—|E| is close to |V|2—or when we need to be able to tell quickly if there is an edge connecting two given vertices.[1]
We'd like to build various graph traversal methods on top of this.
There are really no usage docs of BioD.
Some examples of usage of BioD in Markdown or some other format that isn't code examples.
D
source files. I found it hard to understand without help.It would be nice if there was a single compiled library of BioD without having to refer to where BioD source code is.
BioD needs to have variant graph support
To add both graph representation (nodes and edges) as well as indexing on the nodes.
Implementing the graph and indexing myself and not importing C++ libs but that didn't seem like a smart idea because it would take too much time.
There is still quite a bit of figuring out in the area as evidenced by work on odgi and xg.
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