odgi is a spiritual successor to vg. It includes some new pangenome analysis tools, and some really interesting visualizations.
This PR adds support for odgi output in cactus-pangenome / cactus-graphmap-join for the whole genome (--odgi) and by chromosome (--chrom-og).
The --viz option is added to produce 1D (odgi viz) images for each chromosome. And the --draw option is added to produce 2D (odgi draw) images for each chromosome.
Some things to do before merging:
documentation and tests
try on human-sized chromosomes. odgi doesn't have any special support for subpaths, so there is a question of how well it'll handle path fragments in the clipped graphs. ie will the visualizations be at all useful in these cases?
see if there's anything that can be done to help draw (perhaps by preprocessing / subsetting paths). As it stands, it seems to take a lot of iterations and compute to get decent images of even tiny minigraph-cactus graphs.
odgi is a spiritual successor to vg. It includes some new pangenome analysis tools, and some really interesting visualizations.
This PR adds support for odgi output in
cactus-pangenome / cactus-graphmap-joinfor the whole genome (--odgi) and by chromosome (--chrom-og).The
--vizoption is added to produce 1D (odgi viz) images for each chromosome. And the--drawoption is added to produce 2D (odgi draw) images for each chromosome.Some things to do before merging:
draw(perhaps by preprocessing / subsetting paths). As it stands, it seems to take a lot of iterations and compute to get decent images of even tiny minigraph-cactus graphs.