GFAv1 output

[ekg]

Is it possible to obtain the paths as directed walks through the graph in GFAv1 format?

[nnoll]

It is not currently a feature within the code, as we only implement GFAv1 and not GFAv1.1, however I think this would be easy to add in practice. My only hangup on exposing paths as a directed walk is there is always the reverse-complementation symmetry which means the path taken in reverse (with all pancontigs traversed in the opposite orientation) is also valid.

I will assign this to myself and add the feature time permitting.

[ekg]

I would suggest GFAv1. v1.1 adds a second path type for metadata on paths that seems relevant haplotype panels. This breaks most existing tools for no general benefit.

On Thu, Feb 24, 2022, 18:28 Nicholas Noll @.***> wrote:

It is not currently a feature within the code, as we only implement GFAv1 and not GFAv1.1, however I think this would be easy to add in practice. My only hangup on exposing paths as a directed walk is there is always the reverse-complementation symmetry which means the path taken in reverse (with all pancontigs traversed in the opposite orientation) is also valid.

I will assign this to myself and add the feature time permitting.

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