Erik Garrison
HHGA should be able to take a model in vw format and apply it to a VCF+BAM combination, yielding an annotated VCF where we have applied class labels in some...
This looks like a great project. What's needed for Linux support?
Is it possible to obtain the paths as _directed_ walks through the graph in GFAv1 format?
Just a quick note... The 23andme data is not exactly your genome, but a SNP chip of your genome. It's "some of your genotypes." Or about 0.1% of your genome....
Is it possible to generate the sequence tube map in a standalone way on the command line?
I'm unable to build this using cmake. ``` /home/erik/libbdsg/bin/_deps/pybind11-src/include/pybind11/detail/common.h:112:10: fatal error: Python.h: No such file or directory ``` However, I am able to build odgi, which includes pybind11 bindings and...
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...