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Mistake in GFA links? #586

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dirkjanvw opened this issue Aug 8, 2024 · 0 comments
Open

Mistake in GFA links? #586

dirkjanvw opened this issue Aug 8, 2024 · 0 comments

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@dirkjanvw
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Hi, thanks for the amazing (and fast) tool to handle graphs!

I have been writing some code myself to parse GFA files (v1.0 based on https://github.com/GFA-spec/GFA-spec). However, I found an irregularity in the GFA output of odgi view. This is how I convert my .og files (from Minigraph-Cactus specifically) to GFA:

odgi view -gi /path/to/graph.full.og > graph.mc.gfa

The issue I found is that some of the links implied in the path don't exist. E.g.: a P-line might have the sequence 23231-,23232+ but this does not exist as L-line. When searching myself, I do however find L 23232 - 23231 + 0M; thus with the two nodes switched. I observed this for multiple GFAs created by odgi; but see example yeast-pg.full.og.gz and resulting example yeast.mc.gfa.gz (GZIP'ed as per GitHub's request).

I tested this with someone else's code too to confirm it is not an issue of my own code (using gfatk: https://github.com/tolkit/gfatk):

$ gfatk path -a yeast.mc.gfa 
>DBVPG6044#0#chrI#0
Error: This link: 23231-|23232+ - does not occur in the input GFA. Perhaps re-consider the input path?

By the way, I'm using odgi as installed from bioconda:

$ odgi version
v0.8.6-0-ge647844f

Is this a bug in odgi view and fixable? Or perhaps is it a more common misinterpretation of the GFA v1.0 format?

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