Adding code for lifting over between sequences and the reference genome.

Provides code for going between a sequence that maps to regions of the reference genome (e.g., a transcript) and a reference genome position, and vice versa.
Actually, one more comment: why is this written this way?  I guess I was expecting,
```scala
case class ReferencePositionWithOrientation(ref : String, pos : Long, strand : Boolean) extends ReferencePosition(ref, pos) {
...
}
```

Is it because the ``ReferencePosition`` class itself is a case class?