Sliding window next locus with regions fix

* Add test case that exposed a bug in slidingWindow.nextLocusWithRegions. Upon initialization of a slidingWindow, currentLocus=-1, which can confuse nextLocusWithRegions into having an assertion error when the first read's start is <= halfWindowSize.

* Fixed the bug in SlidingWindow.scala. Also added some more comments.

* Better docs in HasReferenceRegion

This is an attempted fix for #253