3rd test fails sporadically on Jenkins

[glennhickey]

ex: http://jenkins.cgcloud.info/job/toil-vg/1205/testReport/junit/src.toil_vg.test.test_vg/VGCGLTest/test_03_sim_small_mapeval/

src/toil_vg/test/test_vg.py:252: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
src/toil_vg/test/test_vg.py:605: in _assertCallEvalOutput
    self.assertGreaterEqual(float(f1), f1_threshold)
E   AssertionError: nan not greater than or equal to 0.02

[glennhickey]

This (or something like it) is happening all the time now, even locally. This needs to be fixed, and ideally this test would get split up in the process.