Deserializing GBZ can fail when the graph has walks in multiple connected components about gbwtgraph HOT 4 CLOSED

This happens if you build in a vg that uses sdsl-lite commit ffc8ed5337aa0d01cf4f2c60e619a873e0b0ce7d, which is the submodule referenced in gbwt commit 5d0b136a3bc0772d3e02e0e4b261de8d75268e7b, which current master gbwtgraph references.

I tried to "upgrade" vg to the "right" sdsl-lite as referenced in this repo, and it turned out vg had the newer, working version already. When I use sdsl-lite commit d4105e78ea42f8aeacb18a5ec8983430ef6190fb the problem goes away.

Maybe we should drop the submodules from this repo and/or from gbwt? If they don't actually describe versions known to work together, they can cause trouble like this.

from gbwtgraph.

The submodules are only used in the cmake build, which was originally intended for the Debian build of VG. I'm not sure if it's necessary anymore. I try to keep the cmake build up to date, but because I don't really use it myself, it's not properly tested.

from gbwtgraph.

I haven't been able to get the CMake build to build for me.

from gbwtgraph.

It looks like the CMake builds have been broken for both GBWT and GBWTGraph since I reorganized the files in May. As nobody has noticed it until now, it seems safe to assume that nobody needs them anymore.

from gbwtgraph.