graph loading fails

[phiweger]

import pyfrost

g = pyfrost.load('x.gfa', 'x.bfg_colors')

# I failed to find one of the right cookies. Found 0
# Segmentation fault: 11

Not sure about this one ...

[lrvdijk]

Hmm I've seen this happen when the graph was made by Bifrost on another system (and different processor architecture) than the system pyfrost is running on. For example, created a graph on my laptop, uploaded it on the cluster and tried to analyse it => error. When I recreated the graph using Bifrost compiled on the cluster I had no problems reading it.

[GuillaumeHolley]

Do you know if it is a Bifrost issue or a Pyfrost issue? Because I never had this problem before with Bifrost and normally, Bifrost output files are supposed to be architecture independent. So if it a Bifrost issue, I should get on it asap. Also, do you know if the problem is with loading the graph or the colors?

[phiweger]

I created the graph on linux (in a Docker container) and tried to load it w/ pyfrost installed on a Mac. If there is a culprit, I would guess the binary color file might create an issue. The graph gfa file does not give me any problems when I parse it with Python manually. @GuillaumeHolley is there a way to access the colors in Bifrost that is not binary but e.g. text-based?

[lrvdijk]

Don't know yet, definitely wouldn't rule out something in my code. Or maybe differences between Clang/GCC? The error about cookies comes from Roaring, so it's the colors that are giving some trouble.

[phiweger]

and still does after the beta release @lrvdijk

# pip install https://github.com/broadinstitute/pyfrost/releases/download/v0.1.0b1/pyfrost-0.1.0b1.tar.gz
import pyfrost

g = pyfrost.load('graph.gfa', 'graph.bfg_colors')
# TypeError: load() takes 1 positional argument but 2 were given

g = pyfrost.load('graph.gfa')
# I failed to find one of the right cookies. Found 55116354
# Segmentation fault: 11

[lrvdijk]

Hmm I will try to figure this out in the near term