Remove more deprecation warnings; some test nits

You could also use something like a table test for this, if we wanted to leave it as a collection of positions we wanted to test repeatedly:

https://github.com/hammerlab/guacamole/blob/master/src/test/scala/org/bdgenomics/guacamole/callers/SomaticLogOddsVariantCallerSuite.scala#L39-L41

Otherwise  all lgtm