move from `P` to `W` "walks" for GFA output

vgteam / vg

tools for working with genome variation graphs

https://biostars.org/tag/vg/

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move from `P` to `W` "walks" for GFA output #483

Open ekg opened 7 years ago

ekg commented 7 years ago

vg's path format is incompatible with the P namespace in GFA.

As such, I'm proposing an extension to the schema which would allow us to read and write the vg model in GFA.

https://github.com/GFA-spec/GFA-spec/pull/47

If this lands, we'll need to make some minor changes in our output. Also, W includes an offset, which is left out of P in the way we handle paths in GFA now.

edawson commented 7 years ago

I can implement this easily but I'm not pleased that we need to.

ekg commented 7 years ago

Feel free to note this on the PR to the GFA-spec.

On Fri, Sep 23, 2016 at 3:41 PM Eric T. Dawson notifications@github.com wrote:

I can implement this easily but I'm not pleased that we need to.

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