Provide better UI for paths

[asl]

• Model around GAF format: list all paths, some paths queries (like in #4)
• Maybe join with BLAST hits and their paths

@ekg I started to draft better UI for paths. Unfortunately, I cannot check how the things are implemented in gfaestus – while after few hours I was able to compile it, I'm unable to run it.

[ekg]

Sorry that it's hard to run. FWIW, We are rewriting based on waragraph to simplify the GPU related dependencies. But if you have a chance please share your errors with Christian (author).

The key things are being able to go from a node to path positions and from path positions to nodes. That's most of what gfaestus and waragraph (1D, newer) aspire to both implement.

So the desired functionality would be 1) an interface that allows selection of a path name and entry of a path position or range, selecting the nodes in that range and zooming to them, and 2) given a selected node show what paths and step positions are on it.

Bonus would be 3) BED input of many ranges -> colors and or labels on the graph using the same positional mechanisms.

On Mon, Jul 11, 2022, 11:35 Anton Korobeynikov @.***> wrote:

• Model around GAF format: list all paths, some paths queries (like in

  4 https://github.com/asl/BandageNG/issues/4)

• Maybe join with BLAST hits and their paths

@ekg https://github.com/ekg I started to draft better UI for paths. Unfortunately, I cannot check how the things are implemented in gfaestus – while after few hours I was able to compile it, I'm unable to run it.

— Reply to this email directly, view it on GitHub https://github.com/asl/BandageNG/issues/85, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEJNSKCYEASG3KOIWBDVTPTGRANCNFSM53G3YGQQ . You are receiving this because you were mentioned.Message ID: @.***>

[asl]

Thanks!

Sorry that it's hard to run. FWIW, We are rewriting based on waragraph to simplify the GPU related dependencies. But if you have a chance please share your errors with Christian (author).

Sure! But basically relying on Vulkan (for a non-game app) seems to be a culprit here. In the end I received "invalid driver" or something like this w/o clear understanding how to debug / fix.

[ekg]

Yup, it's awkward as a dependency, but Vulkan is what allows gfaestus to provide zoomable views of whole chromosome pangenome graphs with base-level variation. The rewrite in the works rebuilds things on a more portable subset of Vulkan.

Anyway, for this conversation the key thing is the functionality, which is just as well described in the abstract. Does it make sense what I'm suggesting?

[asl]

@ekg Yes, all this make perfect sense! Thanks!

[asl]

@ekg What do to exactly mean as step in given a selected node show what paths and step positions are on it.?

[asl]

Ok, I think you just mean the node positions. This is WIP currently:

[asl]

Path position search is also done:

[asl]

I'm going to keep this open in case more requests / ideas will appear