faster min_node_support when support is 0 #4095
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This Biostars question, actually: https://www.biostars.org/p/9572558/ |
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A thought I just had: someone pointed in this comment that this is a very repetitive genome stemming from LTR transposon activity. Maybe it could have something to do with that? |
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Changelog Entry
To be copied to the draft changelog by merger:
vg callpatched so that certain problem cases no longer take forever.Description
I'm not sure if there's a github issue for this, but I think it comes from here:
https://www.biostars.org/p/9572558/
and @jeizenga was kind enough to pass over the data, with which it is easy to reproduce.
But I still don't really understand what's going on. Usually it boils down to one big snarl, but in this case it just seems to be going a bit slow on every single snarl. And whenever I pause it, it's always inside
PackedTraversalSupportFinder::get_min_node_support()I don't know why this function would cause a slowdown on this particular graph, and I suspect there's something going on that I should be figuring out but am not.
The good news is that there's a fairly obvious speedup: quit computing the min() if 0 is ever found. And... somehow that seems to be enough to get it to run through on this input.