Fixes to sorting in ReferencePosition

When using the ReferencePositionWithOrientation, we were getting the Scala error: `diverging implicit expansion for type scala.math.Ordering[Option[edu.berkeley.cs.amplab.adam.models.ReferencePosition]]`
This is because the Option ordering wasn't implicitly included; this is fixed by importing `Ordering.Option`.

Because of this change, `Option(x)` needs to become `Some()` instead.