||2 years ago|
|README.org||2 years ago|
Notes on the variant/variation graph
In this repository I am recording an exploratory path through the variation graph (VG) also known as variant graph and pangenome. The goal is to come up with a new reference implementation that is (kinda) language agnostic, i.e., more of a documentation effort with implementation(s). The reference implementation aims to support:
Multiple in-memory graph storage solutions
Bindings for languages such as Python, Julia and Racket
Mix data from many sources (short reads, long reads, RNA-seq etc)
Support metadata and annotation
Based on this reference implementation we should be able to build out functionality as modular extension.
Checked out some sources in opensource/vg
ODGI has a python module. Odgi node.cpp and node.hpp contain packing hacked_vector bit packed (hacked pack vector)
libbdsg has a slightly more obvious implementation of the packed graph
GFA2 is overly complicated. Question is how far we need to support it.