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vgteam / long-read-giraffe-experiments

Experimental materials for testing the long-read mapping abilities of vg giraffe
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Stop surjected nanopore reads from unmapping #43

Closed adamnovak closed 2 months ago

adamnovak commented 2 months ago

Only ~60% of nanopore reads seem to be mapped after surjection. It looks like we are hitting a limit on the graph size for the subgraph we surject onto and bailing out. We should probably just limit alignment size instead like Jordan suggests.

adamnovak commented 2 months ago

I think I fixed this in vg a6dfc43d, by just scaling the existing threshold by the read length.