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ggonnella / gfaviz

Graphical interactive tool for the visualization of sequence graphs in GFA format.
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memory usage #64

Open ekg opened 5 years ago

ekg commented 5 years ago

This is more a word of motivation than anything. We desperately need tools that can scale to render whole genome alignment graphs. In my testing, gfaviz has dramatically worse memory performance with respect to graph size than Bandage.

You'll need to move this file to .xz, then unpack and run. It's not very big but it took more RAM than I had available to load (16GB) and crashed gfaviz when loading it in (not when rendering).

seqwish_yeast_l10k.no_paths.gfa.xz.txt

If the problem is about the size of the graph in memory, consider using a succinct graph library like https://github.com/vgteam/dsgvg to hold it in memory.

ggonnella commented 5 years ago

The file is not that huge, so I am sure there is some bug going on. I'll be trying to understand what happens.