Clarification of pinch graph generation in GFA import

Question

[ericco92]

Hi,

I'm ripping out the gfakluge-backed GFA input mechanism in vg and replacing it with one that should be much lighter weight. There has been talk about whether the pinch graph code in gfa.hpp is still needed. Is it? I assume it's to enable input of non-blunt graphs; if we still support this I'll make sure to incorporate all the current code.

Cheers, Eric

Answer 1

[anovak]

I don't think it is needed anymore. I'm pulling it out in https://github.com/vgteam/vg/pull/2720.

The intended way to import a GFA graph with overlaps will then be by first bluntifying it with a tool like Stark that can properly preserve the kmer space of the input graph.