As noted in #4861 (comment), it's possible for the CI tests to simulate reads that BWA-MEM has an unusually difficult time mapping (including reads that end up mismapped at MAPQ 60).
This can make the CI tests fail for reasons unrelated to the branch under test.
We should figure out how to pass a seed through toil-vg for read simulation, and do that, so the tests are deterministic. I don't think, in the last few years, we've ever had those randomized tests fail in a way that let us actually find something to fix.
If it's already seeded to be deterministic, we should figure out why it isn't actually deterministic and fix it.
As noted in #4861 (comment), it's possible for the CI tests to simulate reads that BWA-MEM has an unusually difficult time mapping (including reads that end up mismapped at MAPQ 60).
This can make the CI tests fail for reasons unrelated to the branch under test.
We should figure out how to pass a seed through toil-vg for read simulation, and do that, so the tests are deterministic. I don't think, in the last few years, we've ever had those randomized tests fail in a way that let us actually find something to fix.
If it's already seeded to be deterministic, we should figure out why it isn't actually deterministic and fix it.